Whole cell assays and methods

ABSTRACT

The disclosure provides methods for analysis of disease cell response to a therapeutic agent. In embodiments, a method comprises administering the therapeutic agent to a disease cell sample from the subject in a device that measures at least one physiological parameter of a cell; determining whether a change occurs in the physiologic parameter of the disease cell sample in response to the therapeutic agent as compared to a baseline measurement or the physiological parameter before administration of the therapeutic agent, and selecting the therapeutic agent that results in the change in the at least one physiologic parameter. In embodiments, the disease cells are whole, viable, and/or label free.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/590,731, filed Jan. 6, 2015, which is a continuation of U.S.application Ser. No. 13/494,618, filed Jun. 12, 2012. The contents ofthe aforementioned applications are hereby incorporated herein byreference.

BACKGROUND

Treatment of diseased individuals has made significant progress sincethe discovery that chemicals and exogenous proteins can be effectivehuman therapeutic agents against specific cellular targets. However,there is still significant room for improvement in the treatment of manycommon diseases such as cancer. One of the main drivers of the HumanGenome Project was to discover the genetic causes of diseases, in orderto advance the development and prescription of therapeutic intervention.If reports are to be believed, all human genes have been identifiedthrough the Human Genome Project. Many of these genes have beenstatistically linked to disease in human populations. Yet knowledge ofthe genetic links of a disease or detection of genetic biomarkers doesnot always effectively predict disease course or therapeutic outcome. Sotoo have the genetic links and even the quantification of proteinexpression levels from those genes been very limited in determiningappropriate therapeutic courses.

Petabyte amounts of genetic information have been collected. A greatdeal of statistical and analytical modeling computing power has beenapplied to the genetic data collected to analyze many different types ofdiseases. At least two important facts have emerged from this process.First, a “disease” like breast cancer is heterogeneous in part becausebreast cancer in one individual can be completely different from thesame cancer in another individual in genetic makeup, protein expressionlevels, and response to therapeutic intervention. Second, detection ofcurrent genetic biomarkers has poor predictive value in the majority ofcases.

Contemporary targeted drugs are discovered and developed along a processwith specific limited number of human cell models in mind. Many of thesecell lines are engineered to provide for optimized screeningenvironments of large libraries of potential drugs to select those withdesired activity against a particular cellular target. Employment ofthis process can be misleading as to the efficacy of potential drugs inlight of clinical information indicating that each patient's disease isdifferent from other patients with the same disease. The drug discoveryand development process to date is not very effective at identifyingresponsive humans prior to clinical trials and continues to suffer ahigh failure rate throughout the clinical development process. Many ofthe drugs that are approved through the regulatory clinical developmentprocess that focuses on reducing harm to patients suffer from poorefficacy rates in actual disease patient populations.

Not all disease condition presentations to the clinical physician arisefrom the same cause. In a simple example, inflammation of bone jointscan arise from several sources, some internal, some external, some“genetically linked,” and some with yet unknown causes. The medicalsciences are fairly effective in triaging patients for infectiousdiseases when the external pathogen can be identified properly.Physicians have fewer tools at hand for predicting which of thetherapies that are currently available will lead to reduction ofinflammation from internal causes. Physicians lack the knowledge of howa specific patient's cells are functioning, or more appropriatelymalfunctioning, and how they will respond to one of the manytherapeutics that are available for treating the disease that presentsclinically as “inflammation.” They may know that an aberrant gene ispresent but do not know how that affects the disease course in aspecific patient. They may know specifically how a drug is supposed toact but not why a particular patient may be unresponsive or resistant tothat drug activity.

Patients need better identification of their particular disease causeand better informed decision-making for an effective therapeutic course.Human genome sequencing and other genetic quantification tools haveinformed doctors that each patient's disease is somewhat unique to thatpatient. This information has spawned a whole business aroundpersonalized medicine, where each patient could potentially receive acustomized therapeutic regimen customized for their disease. Drugs arebeing developed for specific gene-related disease indications. Thisideal approach has yet to be validated due primarily to significantshortcomings of the current prognostic toolset. The genes may be presentbut their function in the context of a particular individual is notcorrelated.

One response to the realization that each patient is different and thatmany times therapies fail to effect a positive response, has been thedevelopment of companion diagnostics. This type of diagnostic test isdesigned using contemporary biomarker detection tools to try to identifythose patients that are more likely to respond to a particular drug. Thetest involves looking for increased gene number, gene mutation, oraltered expression level of a particular gene. Success rates for most ofthese tests at predicting significant therapeutic response are oftenmuch less than 50%.

Thus there remains a need to provide better prognostic indicators forthe effectiveness of therapeutics for an individual.

SUMMARY OF THE INVENTION

Some drugs are being targeted for specific gene-related diseaseindications. This approach has not yet been broadly utilized dueprimarily to significant shortcomings of the current prognostic toolset.The kits and methods as described herein provide for a method ofselecting a therapeutic agent that shows efficacy against anindividual's disease. In embodiments, the therapeutic agent is contactedto label free live whole cells from diseased tissue in a CReMS and achange or lack thereof in a physiologic parameter of the cells isdetected in the presence of the therapeutic agent. A therapeutic agentis selected to treat the subject that results in a change in aphysiological parameter of the disease cell as compared to a baselinemeasurement.

One aspect of the disclosure includes methods of selecting one or moretherapeutic agents either at the initial diagnosis or throughouttreatment. In embodiments, a method for selecting one or moretherapeutic agents that are approved for use to treat a disease ordisorder in an individual subject comprises administering one or moretherapeutic agents to at least one isolated disease cell sample from thesubject in a cellular response measurement system; determining whether achange occurs in cellular response parameter of the disease cell samplein response to the therapeutic agent or agents as compared to a baselinemeasurement of the cellular response parameter before administration ofthe therapeutic agent or agents, wherein the change in cellular responseparameter indicates that the agent or agents has therapeutic efficacyfor the disease in the individual subject. In embodiments, the isolateddisease cell sample comprises label free whole cells. In embodiments,the change of the cellular response parameter in the isolated diseasecell is monitored continuously for a defined period of time. Inembodiments, the method further comprises selecting the therapeuticagent or combination of therapeutic agents that results in the change ofat least one cellular response or physiologic parameter andcommunicating the selected agent to a health care provider. Inembodiments, the method further comprises administering the therapeuticagent or combination of therapeutic agents that results in the change ofat least one cellular response or physiologic parameter to the subject.

In embodiments, a method for selecting a treatment for an individualsubject comprises determining therapeutic efficacy of an agent for adisease in the individual subject comprising: administering the agent toat least one isolated label free disease cell sample from the individualsubject in a cellular response measurement system (CReMS), wherein thedisease cell sample is selected from the group consisting of a cancercell sample, a cell sample from a subject with an autoimmune disease, acell sample from a tissue infected with a foreign agent and combinationsthereof; continuously measuring a change in at least one physiologicalresponse parameter of the cell sample for a defined period of time inthe presence of the therapeutic agent; and determining whether a changein a physiological response parameter of the cell sample to the agentoccurs as compared to a baseline measurement, wherein the change inphysiological response indicates that the agent has therapeutic efficacyfor the disease in the individual subject.

In embodiments, a method for selecting a treatment for an individualsubject having cancer comprises determining therapeutic efficacy of anagent for cancer in the individual subject comprising: administering theagent to at least one isolated label free cancer cell sample from theindividual subject in a biosensor; continuously measuring a change in atleast one physiological response parameter of the cell sample for adefined period of time in the presence of the therapeutic agent; andselecting the therapeutic agent for treatment of the subject thatexhibits a change in a physiological response parameter of the cellsample as compared to a baseline measurement.

In another aspect of the disclosure, a kit comprises: a container for adisease cell sample from an individual subject containing a transportmedium; a container for a control cell sample from the individualsubject containing a transport medium; a biosensor; and a non-transitorycomputer readable medium having computer executable instructions forconverting data from the biosensor into an output, wherein the outputshows a change in a cellular physiological response parameter over adefined period of time, wherein the cellular physiological responseparameter is selected from the group consisting of pH, cell adhesion,cell attachment pattern, cell proliferation, cell signaling, cellsurvival, cell density, cell size, cell shape, cell polarity, O₂, CO₂,glucose, and combinations thereof; classifying the output as noresponse, weakly responsive, and responsive; and generating a reportwith the classification.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A, 1B, and 1C show the results of a “CELx” test performed withcells from two HER2 overexpressing breast cancer patients (Patient B1and B4), two targeted pathway drugs (Lapatinib and Trastuzumab) that areindicated for HER2 positive breast cancers, and human epidermal growthfactor (EGF). The physiologic change of the B1 and B4 cells during thetest was measured with a cellular response measurement system (CReMS)and the output from the CReMS is what is recorded in the figure. Onesample each of B1 and B4 cells was pre-treated with Lapatinib andanother sample each of B1 and B4 cells was pre-treated with Trastuzumaband the physiologic response of each set of cells to subsequent EGFstimulation is recorded on a continuous basis throughout the test. TheCELx Pathway Shutdown test shown in FIG. 1A predicts that Patient B1will not respond to trastuzumab but will respond to Lapatinib. Theresults shown in FIG. 1B also predict that Patient B4 would respond toboth trastuzumab and lapatinib. The comparison of the CELx testprediction and the result recorded by third party clinical reference isshown in FIG. 1C; it shows that the CELx test accurately predicted theresults recorded by the clinical reference standard, where Patient B1was found unresponsive to trastuzumab and responsive to lapatinib andPatient B4 was found responsive to both.

FIGS. 2A, 2B, and 2C show the results of a CELx test performed withcells from two breast cancer patients (Patients B1 and B2) and theanti-proliferative drug Paclitaxel. The physiologic change of the B1 andB2 cells during the test was measured with a CReMS and the output fromthe CReMS is what is recorded in the figure. One set each of the B1 andB2 cells were treated with Paclitaxel and another control set of B1 andB2 cells received no drug; the physiological response of each set ofcells was recorded continuously over the course of 48 hours. The B2 testcells showed initial responsiveness to Paclitaxel, as reflected in thesignificant decrease in CReM output compared to the B2 control cells,but after roughly 24 hours, the CReM output reverses, indicating thatthe test cells begin proliferating and are no longer responsive to thedrug. The B1 test cells show immediate and continuous responsiveness toPaclitaxel, as reflected in the decrease in CReM output compared to theB1 control cells throughout the test period. The CELx test resultspresented in FIGS. 2A and 2B predict that both patients B1 and B2 willrespond to paclitaxel. The comparison of the CELx test prediction andthe result recorded by third party clinical reference is shown in FIG.2C; it shows that the CELx test accurately predicted the resultsrecorded by the clinical reference standard, where Patients B1 and B2were both found responsive to paclitaxel.

FIGS. 3A, 3B, and 3C show the results over the entire time course of theexperiment of a CELx test performed with cells from two colon cancerpatients (Patients C1 and C2), EGF, and a combination of two drugsindicated for colon cancer, cetuximab and irinotecan. The physiologicchange of the C1 and C2 cells during the test was measured with a CReMSand the output from the CReMS is what is recorded in the figure. One seteach of C1 and C2 test cells were treated with Cetuximab and Irinotecanand another set of control C1 and C2 cells received no drug; thephysiological response of each set of cells was recorded continuously.Both the C1 and C2 test cells showed responsiveness to the drugcombination as reflected in the reduced CReMS output for the test cellscompared to their respective control cells. These results predict thatboth patients C1 and C2 will respond to the combination of cetuximab andirinotecan. The comparison of the CELx test prediction and the resultrecorded by third party clinical reference is shown in FIG. 3C; it showsthat the CELx test accurately predicted the results recorded by theclinical reference standard, where Patients C1 and C2 were both foundresponsive to the cetuximab and irinotecan combination.

FIG. 4 shows the summary results of 57 CELx tests performed using someof the cell and drug combinations possible from a selection of 11different patient cells (breast cancer cells from Patients B1, B2, B3,B4, B5, B6, B7, colon cancer cells from Patients C1 and C2, and lungcancer cells from Patients L1 and L2) and 15 different drugs(capecitabine, cetuximab, docetaxel, fluorouracil, gefitinib,GSK1059615, GSK1120212, lapatinib, paclitaxel, pazopanib, trastuzumab,topotecan, cisplatin, erlotinib, and oxiliplatin). FIG. 4 also shows theresults from two CELx Combination tests performed using the drugcombination of paclitaxel and cisplatin on Patient L1 and L2 cells andfour CELx tests with the drug combination of trastuzumab and lapatinibon Patient B1, B2, B3, and B4 cells. A total of sixteen different drugsthat target 11 different cellular pathways were introduced to cellsamples in this set of experiments. For each experiment, the change ofthe test cells' physiologic response compared to its control cells wascalculated. Each box in FIG. 4 classifies the change in physiologicresponse measured in each experiment as either being greater than 50%(solid box), between 5%-50%, (vertical shaded box), less than 5%(horizontal shaded box), or not tested (open box). The series ofexperiments represented in this figure illustrate the CELx test'sability to measure the physiologic change that occurs in a variety ofcancer cell types after they are exposed to wide range of drugs.

FIG. 5 shows the summary results of eight CELx tests performedseparately on cells from four breast cancer patients (B1, B2, B3, andB4) with the drug Cetuximab and EGF. One set of tests on cells B1, B2,B3, and B4 was performed using an “Optical” biosensor CReMS and anotherset of tests on the same cells was performed using an “Impedance”biosensor CReMS. The results are presented in a summary fashion showingthe range of percentage change in output recorded by the CReMS. For eachpatient cell tested, the amount of physiologic change recorded by eachCReMS was identical. These results illustrate that the CELx test methodcan utilize different types of CReMS' that measure different physiologicchanges in cells.

FIG. 6 provides the summary results of the 65 tests described inExamples 1-4. A total of 16 different drugs that target 11 differentcellular pathways were introduced in this set of experiments to cellsamples from 11 patients with three different types of cancer. For eachexperiment, the change of the test cells' physiologic response comparedto its baseline, or control cells, was calculated. Each box in FIG. 6classifies the change in physiologic response measured in eachexperiment as either being greater than 50%, between 5%-50%, or lessthan 5%. The CELx test predicts a positive patient response to thetherapy when the change in physiologic response is between 5%-50% orgreater than 50% and it predicts no patient response to the therapy whenthe change in physiologic response is less than 5%. The responses areshown as follows: greater than 50% (solid box), between 5%-50%,(vertical shaded box), less than 5% (horizontal shaded box), or nottested (open box). The series of experiments represented in this figureillustrate the CELx test's ability to measure the physiologic changethat occurs in a variety of cancer cell types after they are exposed towide range of drugs that affect a wide range of cellular pathways.

FIG. 7 records the correlation (either 0% or 100%) between the CELx testpredictions described in FIG. 6 (test cell response to individual drugs)and results from third parties that recorded the patient'sresponsiveness to the drug. The solid boxes represent 100% concordancebetween test results on the cell sample for response or nonresponse tothe therapeutic agent and the known status of the cell sample, a blankbox is not tested, and a gray shaded box represents no concordance withthe known cell sample status for response or non response to thetherapeutic agent. In tested cases, the CELx test and the third partiesgenerated the same result except in one case, illustrating the power ofthe CELx test to predict breast, lung, and colon patient response to 16different drugs that target a wide range of cellular pathways.

FIGS. 8A, 8B, 8C and 8D record the CELx test results for differentpatient cancer cells and drugs versus results from third parties thatrecorded the patient's responsiveness to the drug. FIG. 8A records thecomparison of results for all 12 cancer patient cells and 16 differentdrugs that were tested. FIG. 8B records the comparison of results forthe eight breast cancer patient cells that were tested singly and incombination with thirteen different drugs. FIG. 8C records thecomparison of results for the two different colon cancer patient cellsthat were tested singly and in combination with three different drugs.FIG. 8D records the comparison of results for the two different lungcancer patient cells that were tested singly and in combination withthree different drugs. In each Figure, the CELx tests are shown topredict accurately whether a patient will or will not respond to aparticular drug or combination of drugs except in one case.

FIG. 9 records the sensitivity and specificity of the CELx test for allthe patient cells and drug tested as well as for the sub-groups ofpatients, drugs, pathways, and CReMS types tested. Overall and withineach of the sub-groups studied, the CELx test generated high sensitivity(98%+) and specificity (99.9%+). These results illustrate the predictivepower of the test across different cancer cell types, drug types, CReMStypes, and pathways targeted.

DETAILED DESCRIPTION A. Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as is commonly understood by one of ordinary skillin the art to which this invention belongs. All patents, applications,published applications and other publications referred to herein areincorporated by reference in their entirety. If a definition set forthin this section is contrary to or otherwise inconsistent with adefinition set forth in the patents, applications, publishedapplications and other publications that are herein incorporated byreference, the definition set forth in this section prevails over thedefinition that is incorporated herein by reference. The followingterms, as used herein, are intended to have the following definitions.

The term “about,” as used herein, means approximately, in the region of,roughly, or around. When the term “about” is used in conjunction with anumerical range, it modifies that range by extending the boundariesabove and below the numerical values set forth. In general, the term“about” is used herein to modify a numerical value above and below thestated value by a variance of 10%. In one aspect, the term “about” meansplus or minus 20% of the numerical value of the number with which it isbeing used. Therefore, about 50% means in the range of 45%-55%.Numerical ranges recited herein by endpoints include all numbers andfractions subsumed within that range (e.g. 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.90, 4, and 5).

The term “activator,” “activate,” or “perturbant,” “perturb,”“perturbation” in conjunction with respect to cells refer to thespecific subject or activity of physiologic manipulation of a cell usingreagents, organic molecules, signaling factors, biochemicals, nucleicacids, or proteins that have an effect on cells well known to thosepracticed in the art. The effect refers to any modulation of cellularphysiologic activity and may include but not be limited to up ordown-regulation.

The term “assay” or “assaying” refers to an analysis to determine, forexample, the presence, absence, quantity, extent, kinetics, dynamics, ortype of a target, such as a cell's optical or bioimpedance response uponstimulation with exogenous stimuli (e.g., therapeutic agent).

The terms “attach,” or “attachment,” refer to, for example, a surfacemodifier substance, a cell, a ligand candidate compound, and likeentities of the disclosure, connected to a surface, such as by physicalabsorption, chemical bonding, chemical attraction, and like processes,or combinations thereof. Particularly, “cell attachment,” “celladhesion,” or “cell sample attachment” refer to the binding of cellstogether or interacting to a surface, such as by culturing, orinteracting with a cell anchoring material, or the like.

The term “attachment pattern” refers to observable traits orcharacteristics of a cell or cell sample's connection to a surface. Anattachment pattern can be quantitative, e.g., number of attachmentsites. An attachment pattern can also be qualitative, e.g., preferredmolecular site of attachment to an extracellular matrix.

The term “antibody” is used in the broadest sense and specificallyincludes monoclonal antibodies (including full length monoclonalantibodies), humanized antibodies, chimeric antibodies, multispecificantibodies (e.g., bispecific antibodies), and antibody fragments thatexhibit a desired biological activity or function.

Antibodies can be chimeric, humanized, or human, for example, and can beantigen-binding fragments of these. “Antibody fragments” comprise aportion of a full-length antibody, generally the antigen binding orvariable region thereof. Examples of antibody fragments include Fab,Fab′, F(ab′)₂, and Fv fragments; diabodies; linear antibodies;single-chain antibody molecules; and multispecific antibodies such asbispecific antibodies, for example formed from antibody fragments.“Functional fragments” substantially retain binding to an antigen of thefull-length antibody, and retain a biological activity. Antibodies canbe “armed” or “conjugated” by combining with one or more other drugsthrough covalent or other attachment to achieve greater potency,specificity, and efficacy than the individual drug molecules couldachieve separately.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies of the population are identical exceptfor possible naturally occurring mutations that may be present in minoramounts. Monoclonal antibodies are highly specific, being directedagainst a single antigenic site. Furthermore, in contrast toconventional (polyclonal) antibody preparations that typically includedifferent antibodies directed against different determinants (epitopes),each monoclonal antibody is directed against a single determinant on theantigen. The modifier “monoclonal” indicates the character of theantibody as being obtained from a substantially homogeneous populationof antibodies, and is not to be construed as requiring production of theantibody by any particular method.

“Chimeric” antibodies (immunoglobulins) contain a portion of a heavyand/or light chain identical with or homologous to correspondingsequences in antibodies derived from a particular species or belongingto a particular antibody class or subclass, while the remainder of thechain(s) is identical with or homologous to corresponding sequences inantibodies derived from another species or belonging to another antibodyclass or subclass, as well as fragments of such antibodies, so long asthey exhibit the desired biological activity (U.S. Pat. No. 4,816,567;and Morrison et al., 1984, Proc. Natl. Acad. Sci. USA 81:6851-6855).

The term “humanized antibody”, as used herein, are antibodies thatcontain minimal sequence derived from nonhuman immunoglobulin. For themost part, humanized antibodies are human immunoglobulins (recipient oracceptor antibody) in which variable domain hypervariable regionresidues of the recipient antibody are replaced by hypervariable regionresidues from a nonhuman species (donor antibody), such as mouse, rat,rabbit, or nonhuman primate having the desired specificity, affinity,and capacity. The hypervariable regions can becomplementarity-determining regions (CDRs) defined by sequence (see, forexample Kabat 1991, 1987, 1983), or hypervariable loops (HVLs) definedby structure (see for example, Chothia 1987), or both.

A “biomolecular coating” is a coating on a surface that comprises amolecule that is a naturally occurring biomolecule or biochemical, or abiochemical derived from or based on one or more naturally occurringbiomolecules or biochemicals. For example, a biomolecular coating cancomprise an extracellular matrix component (e.g., fibronectin,collagens, laminins, other glycoproteins, peptides, glycosaminoglycans,proteoglycans, vitronectin, IntercellularCAMs, VascularCAMs, MAdCAMs),or a derivative thereof, or can comprise a biochemical such aspolylysine or polyornithine, which are polymeric molecules based on thenaturally occurring biochemicals lysine and ornithine. Polymericmolecules based on naturally occurring biochemicals such as amino acidscan use isomers or enantiomers of the naturally-occurring biochemicals.Coatings can also include cell surface receptor or cell surface cognatebinding proteins or proteins with affinity for said cell surfaceproteins.

The term “baseline measurement” refers to a physiologic beginning pointfor a set of cells to be tested and is based on an evaluation ofmeasurements over a period of time before drug is added. This mayinclude a basal cellular metabolism measurement or CReMS reading priorto exogenous perturbation. This may alternatively include but not belimited to include the CReMS measurement of a normal healthy cellmetabolic function with or without exogenous perturbation.

The term “basal morphology” refers to the form and structure of a cellor cell sample prior to the introduction of an agent or stimulus.

The term “cell adhesion” refers to the binding of a cell to anothercell, to an extracellular matrix component, or to a surface (e.g.,microtiter plate).

The term “Cellular Response Measurement System” or “CReMS” refers to adevice that can quantitatively determine a change in a physiological orcellular response parameter in a cell, in and between cells, and betweencells and the instrumentation device. In embodiments the cell is a wholelabel free cell. A change in a physiological or cellular responseparameter is measured by determining change in an analyte such asglucose, oxygen, carbon dioxide, amine containing materials such asproteins, amino acids, or of the extracellular matrix, or of a cellsignaling molecule, or of cell proliferation, cell morphology, orcytoskeletal rearrangement. An example of a CReMS is a biosensor.

The term “CReMS Signal” as used herein is defined as a measure ofcellular physiologic change of cells when those cells are analyzed by achemo-electric CReMS. The CReMS signal and changes in the CReMS signalcan have various units as related to the particular chemo-electrictransducer measuring the physiologic change. For example, the CReMSsignal may have units of but not be limited to cell index, impedance,wavelength units, pH units, voltage, current, or become dimensionless byusing ratios of the units. Any of these units may have a time component.The CReMS signal can be mathematically modified for clarity ofinterpretation as is frequently done by those practiced in the art ofbiology, biochemistry and biophysics, for example includingnormalization, baselining, curve subtracting, or any combination ofthese. The CReMS signal may be measured at a single time point, or, morepreferably, over a continuous series of time points representing acomplete pattern of cellular physiologic response.

The term CReM “optical signal” is defined as the wavelength value orchange in wavelength value measured as light is reflected from thephotonic crystal biosensing CReMS upon which the cells rest. The unitsare typically in picometers or nanometers though could also becomedimensionless if ratios of changes are reported. The “optical signal”could be expressed in said units combined with time. The shift inreflected wavelengths of light is proportional to the mass upon thephotonic crystal surface. Thus the “optical signal” is a quantitativemeasure of the number of cells on the CReMS. Furthermore, the “opticalsignal” is a measure of the cell physiological status as for examplechanges in cell morphology, cell adhesion, cell viability, structuralrearrangements of the cell lead to differences in the amount of massupon the sensor that are detected as wavelength shifts.

The term “Cell Index” as used herein is defined as a measurement ofimpedance and can be applied in one instance of the present invention bymeasuring at a fixed electrical frequency of, for example, 10 kHz andfixed voltage.

And calculated by the equation Cell Index_(i)=(R_(tn)−R_(t0))/F

Where:

i=1, 2, or 3 time point

F=15 ohm in one example when the instrument is operated at 10 kHzfrequency

R_(t0) is the background resistance measured at time point T0.

R_(tn) is the resistance measured at a time point Tn following celladdition, cell physiologic change, or cell perturbation.

Cell index is a dimensionless parameter derived as a relative change inmeasured electrical impedance to represent cell status. When cells arenot present or are not well-adhered on the electrodes, the CI is zero.Under the same physiological conditions, when more cells are attached onthe electrodes, the CI values are larger. CI is therefore a quantitativemeasure of cell number present in a well. Additionally, change in a cellphysiological status, for example cell morphology, cell adhesion, orcell viability will lead to a change in CI.

The term “biosensor” refers to a device that measures an analyte or achange in an analyte or physiologic condition of a cell. In embodiments,the biosensor typically contains three parts: a biological component orelement that binds or recognizes the analyte (including non-limitingexamples such as extracellular matrix, cell signaling molecule, or cellproliferation, tissue, cells, metabolites, catabolites, biomolecules,ions, oxygen, carbon dioxide, carbohydrates, proteins etc.), a detectorelement (operating in a physicochemical manner such as optical,piezoelectric, electrochemical, thermometric, or magnetic), and atransducer associated with both components.

The term “optical biosensor” refers to a device that measuresfluorescence, absorption, transmittance, density, refractive index, andreflection of light. In embodiments, an optical biosensor can comprisean optical transducer for converting a molecular recognition ormolecular stimulation event in a living cell, a pathogen, orcombinations thereof into a quantifiable signal. Additionally,embodiments could include a photonic crystal device, an opticalwaveguide device, and a surface plasmon resonance device.

The term “impedance biosensor” refers to a device that measures compleximpedance changes (delta Z, or dZ) of live patient cells where impedance(Z) is related to the ratio of voltage to current as described by Ohm'slaw (Z=V/I). It is sensitive to the local ionic environment at theelectrode interface with the cells and detects these changes as afunction of voltage and current fluctuations. Physiologic changes of thecells as a result of normal function or perturbation thereof result inquantifiable changes to the flow of current around the electrodes andinfluence the magnitude and characteristics of the signal measured. Inembodiments, an impedance biosensor can comprise electrodes or anelectrical circuit for converting a molecular recognition or molecularstimulation event in a living cell, a pathogen, or combinations thereofinto a quantifiable signal. In embodiments, an ISFET biosensor cancomprise an ion selective field effect electrical transducer forconverting an analyte recognition or cellular stimulation event in aliving cell, a pathogen, or combinations thereof into a quantifiablesignal. When an analyte concentration in an ISFET biosensor changes, thecurrent in the transistor changes, which creates a quantificationsignal.

The term “cell signaling” refers to the intracellular or intercellulartransfer of information. Cells signaling can be achieved by directcontact between cells or by the release of a substance from one cellthat is taken up by another cell. Intercellular signaling can occur viaan interaction between two molecules (e.g., a ligand and a receptor).Receptor binding can trigger a cascade of intracellular signaling (e.g.,initiation of biochemical changes within the cell or modification of themembrane potential).

The term “cytoskeletal organization” refers to the arrangement of theinternal scaffold of a cell. A cell's cytoskeleton comprises filamentsthat serve to support cytoplasmic or membrane elements and/orintracellular organelles. The cytoskeleton also helps to maintain theshape of a cell.

The term “cell proliferation” refers to an increase in the number ofcells as a result of cell growth and cell division.

The term “cell survival” refers to the viability of a cell characterizedby the capacity to perform certain functions such as metabolism, growth,movement, reproduction, some form of responsiveness, and adaptability.

The term “efficacy” refers to the extent to which a specificintervention produces a beneficial result. In embodiments, theintervention can be a therapeutic agent, such as a small molecule or anantibody. A beneficial result includes without limitation an inhibitionof symptoms, a decrease in cell growth, an in increase in cell killing,a decrease in inflammation, and an increase in immune responsiveness.

An “extracellular matrix component” is a molecule that occurs in theextracellular matrix of an animal. It can be a component of anextracellular matrix from any species and from any tissue type.Non-limiting examples of extracellular matrix components includelaminins, collagens, fibronectins, other glycoproteins, peptides,glycosaminoglycans, proteoglycans, etc. Extracellular matrix componentscan also include growth factors.

The term “global phenotype” refers to a plurality of observableproperties of a cell or cell sample as a whole. A global pheonotype mayinclude but not be limited to cell size, cell shape, distinctiveprotuberances, outgrowths, spreading, attachment foci density,cytoskeletal arrangements, cell proliferation patterns, receptorphagocytosis, or attachment foci number, changes in pH, uptake or effluxof metabolites, signaling proteins and growth factors, oxygen, CO2,glucose, ATP, and ions such as magnesium, calcium, potassium.

The term “event specificity” refers to a physical observation of aspecific property of a cell. Such specific properties relate to aspecific cellular function, exogenous perturbation, or pathwayagonsim/antagonism as part of the intended and/or expected physiologicalresponse of the cell to a particular activator or therapeutic agent.Activators and therapeutic agents may be known to be targeted to affecta certain aspect of the cell function such as cytoskeletal structure, ora cellular pathway. The physically observable event is called eventspecificity because the physically observable event in the cell in thepresence of the activator or the therapeutic agent is a reflection ofthe intended and/or expected effect the activator or therapeutic agenton the cell. For example, the addition of vinblastine to most cellsamples on an attachment biosensor type of CReMS produces a profoundreduction in signal. Vinblastine is a cellular cytoskeletal scaffoldingdisrupter. The reduction in signal is a physically observable event ofthe cell linked specifically to loss of cell shape and attachment causedby the drug action at microtubule molecules.

The term “Impedance” as used herein is defined by a physical lawrelating voltage and current by the equation: Impedance (ohm)=Voltage(volts)/Current (amperes) or Z=V/I.

“Mammal” for purposes of treatment or therapy refers to any animalclassified as a mammal, including humans, domestic and farm animals, andzoo, sports, or pet animals, such as dogs, horses, cats, cows, and thelike. Preferably, the mammal is human.

The term “microcantilever device”, “microcantilever array”, ormicrocantilever apparatus” refers to a type of CREMS instrumentcomprising at least one cantilever, a flexible beam that may bebar-shaped, V-shaped, or have other shapes, depending on itsapplication. One end of the microcantilever is fixed on a supportingbase, another end standing freely. Microcantilevers can measureconcentrations using electrical methods to detect phase differencesignals that can be matched with natural resonant frequencies (examplesas described in U.S. Pat. No. 6,041,642, issued Mar. 28, 2000, which ishereby incorporated by reference) Determining a concentration of atarget species using a change in resonant properties of amicrocantilever on which a known molecule is disposed, for example, amacromolecular biomolecule such as DNA, RNA, or protein. Deflection ismeasured using optical and piezoelectric methods.

“Polynucleotide,” or “nucleic acid,” as used interchangeably herein,refer to polymers of nucleotides of any length, and include DNA and RNA.The nucleotides can be deoxyribonucleotides, ribonucleotides, modifiednucleotides or bases, and/or their analogs, or any substrate that can beincorporated into a polymer by DNA or RNA polymerase, or by a syntheticreaction. A polynucleotide may comprise modified nucleotides, such asmethylated nucleotides and their analogs. If present, modification tothe nucleotide structure may be imparted before or after assembly of thepolymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter synthesis, such as by conjugation with a label. Other types ofmodifications include, for example, “caps”, substitution of one or moreof the naturally occurring nucleotides with an analog, internucleotidemodifications such as, for example, those with uncharged linkages (e.g.,methyl phosphonates, phosphotriesters, phosphoamidates, carbamates,etc.) and with charged linkages (e.g., phosphorothioates,phosphorodithioates, etc.), those containing pendant moieties, such as,for example, proteins (e.g., nucleases, toxins, antibodies, signalpeptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine,psoralen, etc.), those containing chelators (e.g., metals, radioactivemetals, boron, oxidative metals, etc.), those containing alkylators,those with modified linkages (e.g., alpha anomeric nucleic acids, etc.),as well as unmodified forms of the polynucleotide(s). Further, any ofthe hydroxyl groups ordinarily present in the sugars may be replaced,for example, by phosphonate groups, phosphate groups, protected bystandard protecting groups, or activated to prepare additional linkagesto additional nucleotides, or may be conjugated to solid or semi-solidsupports. The 5′ and 3′ terminal OH can be phosphorylated or substitutedwith amines or organic capping group moieties of from 1 to 20 carbonatoms. Other hydroxyls may also be derivatized to standard protectinggroups. Polynucleotides can also contain analogous forms of ribose ordeoxyribose sugars that are generally known in the art, including, forexample, 2′-O-methyl-, 2′-O-allyl, 2′-fluoro- or 2′-azido-ribose,carbocyclic sugar analogs, alpha-anomeric sugars, epimeric sugars suchas arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars,sedoheptuloses, acyclic analogs and a basic nucleoside analogs such asmethyl riboside. One or more phosphodiester linkages may be replaced byalternative linking groups. These alternative linking groups include,but are not limited to, embodiments wherein phosphate is replaced byP(O)S (“thioate”), P(S)S (“dithioate”), “(O)NR.sub.2 (“amidate”),P(O)R′, P(O)OR′, CO or CH.sub.2 (“formacetal”), in which each R or R′ isindependently H or substituted or unsubstituted alkyl (1-20 C)optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl,cycloalkenyl or araldyl. Not all linkages in a polynucleotide need beidentical. The preceding description applies to all polynucleotidesreferred to herein, including RNA and DNA.

“Polypeptide” refers to a peptide or protein containing two or moreamino acids linked by peptide bonds, and includes peptides, oligimers,proteins, and the like. Polypeptides can contain natural, modified, orsynthetic amino acids. Polypeptides can also be modified naturally, suchas by post-translational processing, or chemically, such as amidation,acylation, cross-linking, and the like.

The term “quartz crystal resonators/microbalance” refers to a type ofCREMS device that measures mass by measuring the change in frequency ofa piezoelectric quartz crystal when it is disturbed by the addition of asmall mass such as a virus or any other tiny object intended to bemeasured. Frequency measurements are easily made to high precision,hence, it is easy to measure small masses.

As used herein, “sample” refers to anything which may contain a moietyto be isolated, manipulated, measured, quantified, detected or analyzedusing apparatuses, microplates or methods in the present disclosure. Thesample may be a biological sample, such as a biological fluid or abiological tissue. Examples of biological fluids include suspension ofcells in a medium such as cell culture medium, urine, blood, plasma,serum, saliva, semen, stool, sputum, cerebral spinal fluid, tears,mucus, amniotic fluid or the like. Biological tissues are aggregates ofcells, usually of a particular kind together with their intercellularsubstance that form one of the structural materials of a human, animal,plant, bacterial, fungal or viral structure, including connective,epithelium, muscle and nerve tissues. Examples of biological tissuesalso include organs, tumors, lymph nodes, arteries and individualcell(s). The biological samples may further include cell suspensions,solutions containing biological molecules (e.g. proteins, enzymes,nucleic acids, carbohydrates, chemical molecules binding to biologicalmolecules).

The term “cell sample” refers to cells isolated from a particularsubject, where the cells are isolated from a subject's biologicalfluids, excretions, or tissues. Cells isolated from tissue can includetumor cells. Cells isolated from tissue include homogenized tissue, andcellular extracts, and combinations thereof. Cell samples includeisolation from, but are not limited to, blood, blood serum, bloodplasma, urine, semen, seminal fluid, seminal plasma, prostatic fluid,pre-ejaculatory fluid (Cowper's fluid), excreta, tears, saliva, sweat,biopsy, ascites, cerebrospinal fluid, lymph, marrow, or hair.

The term “CELx” test refers generally to the various embodiments of themethods described herein.

The term “disease cell sample” refers to a plurality of cells from thesite of disease or cells that have the characteristic of disease.

The term “healthy cell sample” refers to a cell sample wherein the cellsdo not have or are extracted from a tissue that does not have thedisease that is being tested. For example, when a particular subject isbeing tested for the effects of a therapeutic agent against thesubject's breast cancer, non-cancerous cells or cells from non-breasttissue are considered “healthy”. The term “healthy cell sample” is not adetermination or reflection upon the whole health status of the subject.

The term Analytical “Sensitivity” refers to a test or the detectionlimit, and is defined as the lowest quantity differentiated from Zero.(e.g. 95% confidence intervals or 2 standard deviations (SD) above themean of the Zero control are commonly used).

The Term Clinical “Sensitivity” refers to the proportion of subjectswith the target condition in whom the test is positive or how often thetest is positive when the condition of interest is present. Clinical“Sensitivity” of a test is defined as an estimate of accuracy providedby the calculation: 100%×TP/(TP+FN) where TP is the number of TruePositive events for an outcome being tested and FN are the number ofFalse Negatives events, incorrectly determined events as negative.

Clinical “Specificity” refers to the proportion of subjects without thetarget condition in whom the test is negative or how often the test isnegative when the condition of interest is absent. Clinical specificityis estimated by the calculation: 100%×TN/(FP+TN) where TN is the numberof True Negative events for an outcome being tested and FP is the numberof False Positives, incorrectly determined events as positive.

The term “surface plasmon resonance device” refers to an opticalbiosensor type of CReMS that measures binding events of biomolecules ata metal surface by detecting changes in the local refractive index.

The term “therapeutic agent” refers to any synthetic or naturallyoccurring biologically active compound or composition of matter which,when administered to an organism (human or nonhuman animal), induces adesired pharmacologic, immunogenic, and/or physiologic effect by localand/or systemic action. The term encompasses those compounds orchemicals traditionally regarded as drugs, vaccines, andbiopharmaceuticals including molecules such as proteins, peptides,hormones, nucleic acids, gene constructs and the like. The agent may bea biologically active agent used in medical, including veterinary,applications and in agriculture, such as with plants, as well as otherareas. The term therapeutic agent also includes without limitation,medicaments; vitamins; mineral supplements; substances used for thetreatment, prevention, diagnosis, cure or mitigation of disease orillness; or substances which affect the structure or function of thebody; or pro-drugs, which become biologically active or more activeafter they have been placed in a predetermined physiologicalenvironment. Therapeutic agents include, but are not limited to,anticancer therapeutics, antipsychotics, anti-inflammatory agents, andantibiotics.

The term “targeted pathway drug,” “pathway drug,” or “targeted drug,”refers to any molecule or antibody with therapeutic capacity designed tobind to a specific biomolecule (eg. protein) involved in a diseaseprocess, thereby regulating its activity.

The term “anti-proliferative drug,” “anti-proliferative agent,” or“apoptosis inducing drug,” refers to any molecule or antibody withtherapeutic capacity that functions to reduce cell division, reduce cellgrowth, or kill cells. In many cases, the activity of these drugs isdirected towards broad classes of biomolecules (eg. DNA intercalation)involved in normal cellular processes and thus the drug may be lessdiscriminant towards cell disease status.

A “variant” of a polypeptide refers to a polypeptide that contains anamino acid sequence that differs from a reference sequence. Thereference sequence can be a full-length native polypeptide sequence orany other fragment of a full-length polypeptide sequence. In someembodiments, the reference sequence is a variable domain heavy chain orvariable domain light chain consensus sequence. A polypeptide variantgenerally has at least about 80% amino acid sequence identity with thereference sequence.

B. Methods of Selecting or Monitoring Efficacy of a Therapeutic Agent

A disease like cancer is heterogeneous in part because cancer in oneindividual can be completely different from the same cancer in anotherindividual in genetic makeup, protein expression levels, and response totherapeutic intervention. Even diseased tissues can vary considerablyfrom one another in gene expression or gene alterations. For example,metastatic tumors may differ from primary tumors. Human genomesequencing and other genetic quantification tools have informed doctorsthat each patient's disease is somewhat unique to that patient. Thisinformation has spawned a whole business around personalized medicine,where each patient could potentially receive a therapeutic regimencustomized for their disease.

Some drugs are being targeted for specific gene-related diseaseindications. This approach has not yet been broadly utilized dueprimarily to significant shortcomings of the current prognostic toolset.The methods as described herein provide for a method of selecting atherapeutic agent that shows efficacy against an individual's disease.In embodiments, the therapeutic agent is contacted to isolated labelfree live whole cells from diseased tissue in a CReMS and a change orlack thereof in a physiologic parameter of the cells is detected in thepresence of the therapeutic agent. A therapeutic agent is selected totreat the subject that results in a change in a physiological parameterof the disease cell as compared to a baseline measurement.

One aspect of the disclosure includes methods of selecting one or moretherapeutic agents either at the initial diagnosis or throughouttreatment. In embodiments, a method for selecting one or moretherapeutic agents that are approved for use to treat a disease ordisorder in an individual subject comprises administering one or moretherapeutic agents to at least one isolated disease cell sample from thesubject in a cellular response measurement system; determining whether achange occurs in cellular response parameter of the disease cell samplein response to the therapeutic agent or agents as compared to a baselinemeasurement of the cellular response parameter before administration ofthe therapeutic agent or agents, wherein the change in cellular responseparameter indicates that the agent or agents has therapeutic efficacyfor the disease in the individual subject. In embodiments, the isolateddisease cell sample comprises label free whole cells. In embodiments,the change of the cellular response parameter in the isolated diseasecell is monitored continuously for a defined period of time. Inembodiments, the method further comprises selecting the therapeuticagent or combination of therapeutic agents that results in the change ofat least one cellular response or physiologic parameter andcommunicating the selected agent to a health care provider. Inembodiments, the method further comprises administering the therapeuticagent or combination of therapeutic agents that results in the change ofat least one cellular response or physiologic parameter.

In another embodiments, a method for selecting a treatment for anindividual subject comprises determining therapeutic efficacy of anagent for a disease in the individual subject comprising: administeringthe agent to at least one isolated label free disease cell sample fromthe individual subject in a cellular response measurement system(CReMS), wherein the disease cell sample is selected from the groupconsisting of a cancer cell sample, a cell sample from a subject with anautoimmune disease, a cell sample from a tissue infected with a foreignagent and combinations thereof; continuously measuring a change in atleast one physiological response parameter of the cell sample for adefined period of time in the presence and/or absence of the therapeuticagent; and determining whether a change in a physiological responseparameter of the cell sample to the agent occurs as compared to abaseline measurement, wherein the change in physiological responseindicates that the agent has therapeutic efficacy for the disease in theindividual subject. In embodiments, the disease cells are cancer cells.

In other embodiments, a method for comparing efficacy of therapeuticagents for a particular subject comprises administering at least twodifferent therapeutic agents to separate disease cell samples from thesame subject in a device that measures at least one physiologicalparameter of a cell; determining the physiologic response of each cellsample to each of the therapeutic agents compared to a baselinemeasurement, wherein the physiologic response indicates efficacy of eachtherapeutic agent. In embodiments, the isolated disease cell samplecomprises label free whole cells. In embodiments, the change of thecellular response parameter in the isolated disease cell is monitoredcontinuously for a defined period of time. In embodiments, the methodfurther comprises selecting the therapeutic agent or combination oftherapeutic agents that results in better efficacy; and communicatingthe selection to a health care provider. In embodiments, the methodfurther comprises administering the therapeutic agent or combination oftherapeutic agents that results in the better efficacy to the subject.

Another aspect of the disclosure provides a method to determine thegrowth rate of tumor cells. By measuring the growth rate of tumors, atreatment can be selected depending on how fast the tumor cells cangrow. If the tumor cells are a fast growing tumor, the health careworker would select a more aggressive treatment as compared to that of atreatment for a slower growing tumor. In embodiments, a method comprisesproviding an isolated tumor cell sample in a cellular responsemeasurement system, monitoring the growth rate of the tumor cell samplecontinuously over a defined period of time, and selecting a moreaggressive treatment for those tumor cells that exhibit a fast growthrate and/or communicating the selected treatment to a health careprovider. In embodiments, the isolated disease cell sample compriseslabel free whole cells. In embodiments, the method further comprisesadministering the selected treatment to the subject. In embodiments, afast growing tumor has a cell doubling rate of less than about 100hours, preferably less than 20 hours, whereas a slower growing tumor hasa cell doubling rate that is 100 hours or more, where the cell doublingrate is the time for one cell to divide into two cells.

In another aspect of the disclosure, provides a method for determiningwhether a particular pathway is active in a disease cell sample from anindividual subject, and or whether the particular pathway is sensitiveto a therapeutic agent to detect the presence of the pathway in thedisease cell sample. In such methods, a profile of cellular pathwaysfunctioning in the disease cell sample of the individual can be obtainedand monitored over time as treatment continues. In embodiments, a methodfor characterizing a disease cell sample for the presence or absence ofa pathway comprises administering one or more activator agents and/ortherapeutic agent to at least one isolated disease cell sample from thesubject in a cellular response measurement system; determining whether achange occurs in cellular response parameter of the disease cell samplein response to the activator agent and/or therapeutic agent as comparedto a baseline measurement of the cellular response parameter beforeadministration of the activator agent and/or therapeutic agent, whereinthe change in cellular response parameter indicates that the cellularpathway activated by the activator agent or inhibited by the therapeuticagent is functioning in the isolated disease cell sample from theindividual subject. In embodiments, the activator agents include growthfactors, protein or other ligands that bind to receptors and cellsurface proteins such as heregulin that then activate cellular pathways,cells including transformed cells that have cell surface receptors thatactivate pathways in a disease cell sample, or small organic molecules(10,000 Daltons or less), peptides, nucleic acids (eg. interfering RNA)that intracellularly perturb cellular physiologic function in a desiredmanner. In embodiments, the therapeutic agents include from anon-limiting list those that inhibit growth factor receptors such asEGFR, Her2, PDGFR, TGFR, FGFR, TNFR, or VEGF receptors, topoisomeraseactivity, kinases, G-protein coupled receptors, receptor tyrosinekinases, microtubule polymerization, cytoskeletal organization, cellfunction and cell adhesion.

In embodiments, a method comprises administering one or more activatoragents to an isolated disease cell sample from the subject in a cellularresponse measurement system; determining whether a change occurs incellular response parameter of the disease cell sample in response tothe activator agent over a defined period of time as compared to abaseline measurement of the cellular response parameter beforeadministration of the activator agent, administering one or moretherapeutic agents to the isolated disease cell sample and determiningwhether a change occurs in cellular response parameter of the diseasecell sample in response to the therapeutic agent over a defined periodof time as compared to the cellular response parameter before or afteradministration of the activator agent, wherein the change in cellularresponse parameter indicates that the cellular pathway activated by theactivator agent and inhibited by the therapeutic agent is functioning inthe isolated disease cell sample from the individual subject.

Additional embodiments include a method for selecting a subject for atreatment, a clinical trial, and/or evaluating the responsiveness ofpatients to a candidate therapeutic agent. In embodiments, the subjectis selected prior to the clinical trial of that candidate therapeutic inorder to select only those patients who are most likely to respond tothe candidate therapeutic; this approach would increase the likelihoodthat the candidate therapeutic could demonstrate efficacy within theselected patient population sufficient to warrant regulatory approval,particularly with therapeutic agents that can only provide anefficacious result for a portion of the overall population that isdiagnosed with that disease. Patients considered for a clinical trial ofan unapproved therapeutic under this approach would have their diseasedcells evaluated to determine their responsiveness to the drug. Onlythose that demonstrate responsiveness to the unapproved therapeuticagent would get selected for the trial. In other embodiments, a subjectis selected for a treatment when a sample of the subject's cells isidentified as a responder by a method comprising administering one ormore therapeutic agents to at least one isolated disease cell samplefrom the subject in a cellular response measurement system; determiningwhether a change occurs in cellular response parameter of the diseasecell sample in response to the therapeutic agent or agents as comparedto a baseline measurement of the cellular response parameter beforeadministration of the therapeutic agent or agents, wherein the change incellular response parameter indicates that the agent or agents hastherapeutic efficacy for the disease in the individual subject. Inembodiments, a method further comprises selecting the subject whosecells exhibit a change in a cellular response parameter in response tothe therapeutic agent or agents for treatment or for a clinical trial.

A further aspect includes a method to identify biomarkers of diseasesample from a subject that demonstrates responsiveness or nonresponsiveness to a therapeutic agent. In embodiments, a method involvescontacting an isolated disease cell sample from a subject with atherapeutic agent in a cellular response measurement system; determiningwhether a change occurs in cellular response parameter of the diseasecell sample in response to the therapeutic agent or agents as comparedto a baseline measurement of the cellular response parameter beforeadministration of the therapeutic agent or agents, wherein the change incellular response parameter indicates that the agent or agents hastherapeutic efficacy for the disease in the individual subject(responder) and lack of a change indicates that the therapeutic agentdoes not have efficacy for that subject's disease (nonresponder). Inembodiments, the method further comprises further characterizing cellsfrom a subject that are responsive to the therapeutic agent for otherbiomarkers and/or further characterizing cells from a subject that arenot responsive to the therapeutic agent for other biomarkers. Inembodiments, other biomarkers comprise gene mutations, single nucleotidepolymorphisms, gene expression levels, proteins, protein mutations,splice variants, cell surface markers, overexpression of a protein ornucleic acid, amplification of a nucleic acid, cell morphology, andcombinations thereof.

In yet other embodiments, a method for determining an optimaltherapeutic regime or combination of drugs for a particular subjectcomprises administering a plurality of therapeutic agent combinations toseparate disease cell samples from the same subject in a device thatmeasures at least one physiological parameter of a cell, wherein eachtherapeutic combination is administered to a separate disease cellsample from the same subject; and determining the physiologic responseof each cell sample to each therapeutic combination compared to abaseline measurement, wherein the physiologic response indicates themost efficacious therapeutic combination of potential therapeuticcombinations. In embodiments, the method further comprises selecting thetherapeutic agent or combination of therapeutic agents that results inthe change of at least one cellular response or physiologic parameter.In embodiments, the method further comprises administering thetherapeutic agent or combination of therapeutic agents that results inthe change of at least one cellular response or physiologic parameter tothe subject.

In another aspect, a method comprises treating a patient for a diseaseby selecting a therapeutic agent for treating the disease comprisingadministering one or more therapeutic agents to at least one isolateddisease cell sample from the subject in a cellular response measurementsystem; determining whether a change occurs in cellular responseparameter of the disease cell sample in response to the therapeuticagent or agents as compared to a baseline measurement of the cellularresponse parameter before administration of the therapeutic agent oragents, selecting the therapeutic agent that causes a change in cellularresponse parameter; administering the therapeutic agent that results inthe change of at least one cellular response or physiologic parameter tothe subject. Therapeutic agents include those that are targeted to aspecific biological pathway, those that inhibit cell proliferation,those that enhance cell killing, those that inhibit inflammation, thosethat kill microorganisms and/or those that enhance an immune response.In embodiments, where the therapeutic agent is targeted to a specificbiological pathway, it may interact with a cell surface receptor andinhibit the action of the ligand for the receptor. For example, somebreast cancer cells are positive for an epidermal growth factor receptor(EGFR) and respond to epidermal growth factor (EGF). The efficacy of atherapeutic agent that inhibits the interaction of EGF for an individualsubject's cells can be determined in the presence and absence of theligand.

In other embodiments, the therapeutic agent inhibits cell proliferationand/or cell killing. In those cases, a rate of change in a cellularresponse or physiological parameter can be measured on a sample and isindicative of the therapeutic agent's efficacy for causing cell death orinhibiting cell proliferation. In embodiments, the rate of change of acellular response is determined in the presence and/or absence of thetherapeutic agent and a known agent that enhances proliferation and/orinhibits cell killing.

In other aspects of the disclosure, kits are provided. In embodiments, akit comprises: a container for a disease cell sample from an individualsubject containing a transport medium; a container for a control cellsample containing a transport medium; a biosensor; and a non transitorycomputer readable medium having computer executable instructions forconverting data from the biosensor into an output, wherein the outputshows a change in a cellular physiological response parameter over adefined period of time, wherein the cellular physiological responseparameter is selected from the group consisting of pH, cell adhesion,cell attachment pattern, cell proliferation, cell signaling, cellsurvival, cell density, cell size, cell shape, cell polarity, O₂, CO₂,glucose, and combinations thereof; classifying the output as noresponse, weakly responsive, and responsive; and generating a reportwith the classification.

Cell Samples

Embodiments of the invention include systems, kits, and methods todetermine the effectiveness of a therapeutic, monitor the effectiveness,or identify a dose of a therapeutic when administered to a subject'sdiseased cells.

Traditionally, disease has been classified by the tissue or organ thatthe disease affects. Due to better knowledge of the underlyingmechanisms (e.g., genetic, autoimmune response, etc.), we now understandthat diseases which affect the same tissue/organ, produce the samesymptoms, etc., may have different etiologies and may have heterogeneousgene expression profiles. In addition, it has been shown in manydiseases that there are responders and non-responders to therapeuticagents. In embodiments, any disease type, for which responders andnon-responders are identified, can be employed in the methods herein inorder to predict or prognosticate whether a particular therapeutic drugcombination of drugs will be effective for a particular individual, e.g.a determination whether the individual is a responder or anon-responder.

One example of a disease type that is known to be heterogeneous innature and to have responders and many non-responders is cancer. Canceris typically classified according to tissue type. However, a moreaccurate description of the heterogeneity of cancer is reflected in thedifferent mutations of the different cancers. An even more accuratedescription of the heterogenity of cancer is the actual functional,physiological result of the mutation in a particular patient's cells.For instance, prostate cancer has different types and differentmutations that cause cancer of this organ. Outcomes and treatments canbe different based on whether the mutation causing the cancer is a gainof function (e.g., proto-oncogene causing increase protein production)or loss of function mutation (e.g., tumor suppressor) and in which gene.Due to the heterogeneity of a particular cancer, it would be expectedthat there would a heterogeneous response to a particular therapeuticagent. Embodiments of this invention allow the testing of a particularsubject's cancer cells to a therapeutic agent or a panel of therapeuticagents to determine the efficacy of a specific therapeutic agent or themost effective therapeutic agent for a particular subject's cancer toselect a treatment for the subject.

Embodiments of the invention include disease cell samples of cancercells from individual subjects. Such cancer cells can be derived from,but not limited to, Acute Lymphoblastic Leukemia (ALL), Acute MyeloidLeukemia (AML), Adrenocortical Carcinoma, Anal Cancer, Appendix Cancer,Astrocytomas, basal cell carcinoma, Extrahepatic Bile Duct Cancer,Bladder Cancer, Bone Cancer, Osteosarcoma, Malignant FibrousHistiocytoma, Brain Stem Glioma, Central Nervous System AtypicalTeratoid/Rhabdoid Tumor, Central Nervous System Embryonal Tumors,Central Nervous System Germ Cell Tumors, Craniopharyngioma,Ependymoblastoma, Ependymoma, Medulloblastoma, Medulloepithelioma,breast cancer, Pineal Parenchymal Tumors of IntermediateDifferentiation, Supratentorial Primitive Neuroectodermal Tumors,Pineoblastoma, Bronchial Tumors, Carcinoid Tumor, Cervical Cancer,Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML),Chronic Myeloproliferative Disorders, Colon Cancer, Colorectal Cancer,Cutaneous T-Cell Lymphoma, Ductal Carcinoma In Situ (DCIS), EndometrialCancer, Esophageal Cancer, Esthesioneuroblastoma, Ewing Sarcoma,Extragonadal Germ Cell Tumor, Intraocular Melanoma, Retinoblastoma,fibrous histocytoma, Gallbladder Cancer, Gastric Cancer,Gastrointestinal Carcinoid Tumor, Gastrointestinal Stromal Tumors(GIST), Gestational Trophoblastic Tumor, Glioma, Hairy Cell Leukemia,Heart Cancer, Hepatocellular Cancer, Langerhans Cell Histiocytosis,Hodgkin Lymphoma, Hypopharyngeal Cancer, islet cell tumors, Kaposisarcoma, renal cell cancer, Laryngeal Cancer, Lip Cancer, Liver Cancer,Lobular Carcinoma In Situ (LCIS), Lung Cancer, Merkel cell carcinoma,Melanoma, mesothelioma, mouth cancer, multiple myeloma, Nasal Cavity andParanasal Sinus Cancer, Nasopharyngeal Cancer. Neuroblastoma,Non-Hodgkin Lymphoma, Non-Small Cell Lung Cancer, Oral Cavity Cancer,Oropharyngeal Cancer, Ovarian Cancer, Pancreatic Cancer, Papillomatosis,Paraganglioma, Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer,Pheochromocytoma, Pineal Parenchymal, Pituitary Tumor, PleuropulmonaryBlastoma, Prostate Cancer, rectal cancer, rhabdomyosarcoma, salivarygland cancer, squamous cell carcinoma, small intestinal cancer,testicular cancer, throat cancer, thyroid cancer, ureter cancer,urethral cancer, uterine cancer, vaginal cancer, vulvar cancer, andWilm's tumor.

Autoimmune diseases are characterized by increased inflammation due toimmune system activation against self antigens. Current therapies targetimmune system cells such as B cells and inflammatory molecules such asanti TNFα. Therapies can be broadly characterized as immune modulatingor immunosuppressant. Drugs may be targeted to particular molecules suchas TNF alpha, Integrins, sphingosine receptors, and interleukins. Otherdrugs act as anti-inflammatory agents such as corticosteroids. In yetother cases, drugs are immunosuppressants such as mercaptopurines andcyclophosphamide. With respect to autoimmune conditions, peripheralblood cells may be examined for the response to a certain therapeutic.In other embodiments, tissue samples of the site of inflammation, forexample, synovial tissue in rheumatoid arthritis or colon tissue forulcerative colitis.

For example, some patients with rheumatoid arthritis are known to benon-responders to anti-TNFα antibodies. In an embodiment, peripheralblood cells can be obtained from a patient suspected as having RA and adecrease in cell signaling ability of the patient's TNF Receptor andassociated MAPK pathway can be used to determine whether the patient islikely to be a responder or non-responder to an immunomodulating orimmunosuppressant compound. Likewise other therapeutics such as thosetargeting to IL-6, Interferon alpha, Interferon gamma, and the like maybe tested in the same way. In other embodiments, it is known thatpatients that have multiple sclerosis are nonresponders to interferonbeta. Cell samples from subjects can be tested against a panel of drugsto see which if any of the drugs are effective for a particular subjectby inducing a change in a cellular physiological parameter. Examples ofadvantageous outcomes would be a reduction in cellular inflammationparameters, as determined by the American College of Rheumatology (ACR)criteria or an increase in cell adhesion for strengthening theblood-brain barrier function.

In other embodiments, patients may have a disease caused by infection ofcells by a microorganism, a foreign body, or a foreign agent. Bloodcells or tissue samples infected with a microorganism may be evaluatedfor responsiveness to various antibiotics, antivirals, or othertherapeutic candidates. For example, there are a number of differenttherapeutic agents for hepatitis C infection that reduce viral function,infected tissue samples can be contacted with one or more therapeuticagents and a change in a cellular physiological parameter is detected.Therapeutic agents are selected that provide a change in a cellularphysiological parameter of the infected tissue, and/or a therapeuticagent that provides a change in a cellular physiological parameter atthe lowest dose. Outcomes such as increase in cell survival or increasein cell growth would be considered advantageous. In other embodimentswhere the therapeutic is designed to effect the human cell directly suchas by blocking viral entry via a specific receptor type or perturbationof a cellular pathway, the patient cell could be tested for receptorbinding or pathway perturbation by said therapeutic as described inother embodiments herein.

In embodiments, the cell samples can be obtained before therapy isinitiated, during therapy, after therapy, during remission, and uponrelapse. The methods as described herein are useful to predicttherapeutic efficacy prior to treatment, during treatment, when apatient develops resistance, and upon relapse. The methods of thedisclosure are also useful as to predict responders or non-responders toa therapeutic agent or combination of agents.

In embodiments, the cells are not contacted or treated with any kind offixative, or embedded in paraffin or other material, or any detectablelabel. In embodiments, it is preferred that the cells remain whole,viable and/or label free. In some embodiments, a cell sample is providedfor both the diseased tissue and healthy tissue. In some embodiments,the cell sample is provided in both viable and fixed form. A cell sampleprovided in fixed form can serve as a control for comparison to theviable cells that are analyzed in accord with the methods as describedherein particularly for improved identification and correlation ofadditional biomarkers.

In embodiments of the invention, cells from an individual subject areused to determine therapeutic effectiveness. Cells can be collected andisolated by well-known methods (i.e., swab, biopsy, etc.). Both diseasedand non-diseased cells can be used. Non-diseased cells can be used as anegative control, a baseline measure, a comparison for measures overtime, etc. In embodiments, a control sample of tissue cells from thesame subject may also be obtained. A control sample may be taken fromanother healthy tissue in the subject or from healthy tissue from thesame organ as the diseased tissue sample. Diseased cells are cellsextracted from a tissue with active disease. In an embodiment, diseasedcells can be tumor cells, such as breast cancer cells. Cancerous cellsdo not necessarily have to be extracted from a tumor. For instance,leukemic cells can be collected from the blood of a patient withleukemia. Cells can be collected from different tissue sites such as thesites of metastasis, circulating tumor cells, primary tumor sites, andrecurrent tumor sites, and cellular responsiveness compared to oneanother. In another embodiment, diseased cells can be extracted from asite of autoimmune disease, such as rheumatoid arthritis.

In embodiments, the number of cells in each tissue sample is preferablyat least about 5000 cells. In embodiments, the cell number in the tissuesample may range from about 5000 to 1 million cells or greater. Cellsamples include isolation from, but are not limited to, blood, bloodserum, blood plasma, urine, semen, seminal fluid, seminal plasma,prostatic fluid, pre-ejaculatory fluid (Cowper's fluid), excreta, tears,saliva, sweat, biopsy, ascites, cerebrospinal fluid, lymph, marrow, orhair.

In an embodiment, the extraction of cells from a subject is at the samelocation as the CReMS (e.g., laboratory, hospital). As such, the cellscan be suspended or preserved in a well-known transfer medium to bridgethe time from subject to biosensor. In another embodiment, theextraction of cells from a subject is at a different location from theCReMS. Once obtained the cell samples are maintained in a medium thatretains the cell viability. Depending on the length of time fortransportation to the site of analysis, different media may employed. Inembodiments, when transportation of the tissue sample may require up to10 hours, the media has an osmolality of less than 400 mosm/L andcomprises Na+, K+, Mg+, Cl—, Ca+2, glucose, glutamine, histidine,mannitol, and tryptophan, penicillin, streptomycin, contains essentialamino acids and may additionally contain non-essential amino acids,vitamins, other organic compounds, trace minerals and inorganic salts,serum, cell extracts, or growth factors, insulin, transferrin, sodiumselenite, hydrocortisone, ethanolamine, phosphophorylethanoloamine,tridothyronine, sodium pyruvate, L-glutamine, to support theproliferation and plating efficiency of human primary cells. Examples ofsuch a media include Celsior media, Roswell Park Memorial Institutemedium (RPMI), Hanks Buffered Saline, and McCoy's 5A, Eagle's EssentialMinimal Media (EMEM), Dulbecco's modified Eagle's medium (DMEM),Leibovitz L-15, or modifications thereof for the practice of primarycell care. In embodiments, the media and containers are endotoxin free,nonpyrogenic and DNase- and RNase-free.

Cellular Response Measurement System (“CReMS”)

Systems and methods of the invention utilize a cellular responsemeasurement system (CReMS). CReMS refers to a device that canquantitatively determine a change in a physiological parameter in acell, in and between cells, and between cells and the instrumentationdevice. A change in a physiological parameter is measured by determiningchange in an analyte (including non-limiting examples such asextracellular matrix, cell signaling molecule, or cell proliferation,tissue, cells, metabolites, catabolites, biomolecules, ions, oxygen,carbon dioxide, carbohydrates, proteins etc.). In embodiments, thebiosensor is measuring a change in the physiological parameter inisolated whole label free viable cells. In embodiments, a biosensor isselected that can measure an expected change due to the type oftherapeutic and/or activator agent.

An example of a CReMS is a biosensor. Examples of biosensors areelectrochemical biosensors, electrical biosensors, optical biosensors,mass sensitive biosensors, thermal biosensors, and ISFET biosensors.Electrochemical biosensors measure potentiometric, amperometric and/orvoltametric properties. Electrical biosensors measure surfaceconductivity, impedance, resistance or electrolyte conductivity. Opticalbiosensors measure fluorescence, absorption, transmittance, density,refractive index, and reflection. Mass sensitive biosensors measureresonance frequency of piezocrystals. Thermal biosensors measure heat ofreaction and adsorption. ISFET biosensors measure ions, elements, andsimple molecules like oxygen, carbon dioxide, glucose, and othermetabolites of interest in the life sciences. In embodiments, thebiosensor is selected from the group consisting of an impedance device,a photonic crystal device, an optical waveguide device, a surfaceplasmon resonance device, quartz crystal resonators/microbalances, and amicrocantilever device. In embodiments, an optical biosensor cancomprise an optical transducer for converting a molecular recognition ormolecular stimulation event in a living cell, a pathogen, orcombinations thereof. In a specific embodiment, the device is animpedance device.

In an example of a biosensor used to measure protein or other in vitrobiomolecular interactions, the capture of a specific protein mass istranslated into meaningful biochemical and biophysical values. Applyinga simple calculation with the captured mass involving the molecularweight of the specific protein captured, the number of moles areevaluated, leading to equilibrium binding constants and otherinteraction descriptive values known to those experienced in the art. Inan example of a biosensor used for cell assays, specific adhesionmolecules on the cell surface modulate their attachment and morphologyclose to the surface of the sensor and other nearby cells uponapplication of external chemical or other stimulus via specific cellularpathways.

The biosensor can detect these modulations that can be selected in sucha way as to be unique to the stimulus and pathway within the cellemployed to respond to stimuli. When designed properly, the biosensorresult for said cell assay can be exquisitely quantitative in molecularand functional terms. Said biosensor result can be a temporal pattern ofresponse for further uniqueness. Biomolecular activators or perturbantsknown to turn on and turn off specific pathways within the cell can beused as controls for determining the specificity of the CReMS biosensorsignal. Methods for curve deconvolution of the temporal response of thebiosensor result (e.g. non-linear Euclidean comparison with controlresponses) can be applied to further more finely detail specificcellular responses. Use of titrating external stimuli in a cellularbiosensor assay can also provide further biochemical and biophysicalparameter description.

One example of a label-free sensor is a high frequency quartz resonatoror quartz crystal microbalance (QCM) or resonating cantilever. Theresonator includes a quartz crystal with a patterned metal electrodeupon its surface. The quartz material has well-characterized resonanceproperties when a voltage is applied. By applying an alternating voltageto the electrodes at a particular frequency, the crystal will oscillateat a characteristic frequency. The oscillation frequency is modulated inquantitative ways when mass is captured on the sensor surface;additional mass results in lower resonator frequency. Therefore, bymeasuring small changes in the resonant frequency of the quartzoscillator, very small changes in deposited mass can be measured withoutattaching a label to the biomolecule or cell under study.

Ion Selective Field Effect Transistor (ISFET) devices are miniaturized,nanoscale, devices that are capable of measuring selected ions,elements, and simple molecules like oxygen, carbon dioxide, glucose, andother metabolites of interest in the life sciences. They have beenextensively described at the electromechanical operational level as wellas at the bioapplication level. To date they have not been described forthe use with a specific patient's cells to discern response orresistance or temporal patterns thereof to proposed therapeuticintervention in disease processes.

Optical biosensors are designed to produce a measurable change in somecharacteristic of light that is coupled to the sensor surface. Theadvantage of this approach is that a direct physical connection betweenthe excitation source (the source of illumination of the sensor), thedetection transducer (a device that gathers reflected or transmittedlight), and the transducer surface itself is not required. In otherwords, there is no need for electrical connections to an opticalbiosensor, simplifying methods for interfacing the sensor with fluidrequired for stabilizing and studying most biological systems. Ratherthan detecting mass directly, all optical biosensors rely on thedielectric permittivity of detected substances to produce a measurablesignal. The changes in dielectric permittivity are related to thedifference in ratio of the speed of light in free space to that in themedium. This change essentially represents the refractive index of themedium. The refractive index is formally defined as the square root ofthe dielectric constant of a medium (see Maxwell's equation for moreexplicit treatment of this relationship). An optical biosensor relies onthe fact that all biological material, such as proteins, cells, and DNA,have a dielectric constant that is higher than that of free space.Therefore, these materials all possess the intrinsic ability to slowdown the speed of light that passes through them. The optical biosensorsare designed to translate changes in the propagation speed of lightthrough a medium that contains biological material into a quantifiablesignal that is proportional to the amount of biological material that iscaptured on the sensor surface.

Different types of optical biosensors include but are not limited toellipsometers, surface plasmon resonant (SPR) devices, imaging SPRdevices, grating coupled imaging SPR devices, holographic biosensors,interference biosensors, Reflectometric Interference Spectroscopy(RIFS), Colorimetric Interference Biosensors, DifferenceInterferometers, Hartman Interferometers, Dual PolarizationInterferometers (DPI), Waveguide sensor chips, Integrated Input GratingCoupler devices, Chirped Waveguide Grating devices, Photonic crystaldevices, Guided Mode Resonant Filter devices based upon Wood'sAnomalies, Trianglular Silver Particle Arrays. And further includedevices that measure a variety of wavelengths of the electromagneticspectrum including but not limited to visible, ultraviolet, nearinfrared, and infrared. The modes of operation include but are notlimited to scattering, inelastic scattering, reflection, absorbance,Raman, transmittance, transverse electric wave, and transverse magneticwave.

The surface plasmon resonance device is an optical biosensor thatmeasures binding events of biomolecules at a metal surface by detectingchanges in the local refractive index. In general, a high-throughput SPRinstrument consists of an auto-sampling robot, a high resolution CCD(charge-coupled device) camera, and gold or silver-coated glass slidechips each with more than 4 array cells embedded in a plastic supportplatform. SPR technology exploits surface plasmons (specialelectromagnetic waves) that can be excited at certain metal interfaces,most notably silver and gold. When incident light is coupled with themetal interface at angles greater than the critical angle, the reflectedlight exhibits a sharp attenuation (SPR minimum) in reflectivity owingto the resonant transfer of energy from the incident light to a surfaceplasmon. Binding of biomolecules at the surface changes the localrefractive index and results in a shift of the SPR minimum. Bymonitoring changes in the SPR signal, it is possible to measure bindingactivities at the surface in real time.

Since SPR measurements are based on refractive index changes, detectionof an analyte is label free and direct. The analyte does not require anyspecial characteristics or labels (radioactive or fluorescent) and canbe detected directly, without the need for multistep detectionprotocols. Measurements can be performed in real time, allowingcollection of kinetic data and thermodynamic data. Lastly, SPR iscapable of detecting a multitude of analytes over a wide range ofmolecular weights and binding affinities. Thus, SPR technology is quiteuseful as a cellular response measurement system.

A CReMS for the measurement of complex impedance changes (delta Z, ordZ) of live patient cells is described in this embodiment whereimpedance (Z) is related to the ratio of voltage to current as describedby Ohm's law (Z=V/I). For example a constant voltage is applied toelectrodes to which patient cells are attached, producing a current thatat differential frequencies flows around, between cells and throughcells. This CReMS is sensitive to the local ionic environment at theelectrode interface with the cells and detects these changes as afunction of voltage and current fluctuations. Physiologic changes of thecells as a result of normal function or perturbation thereof result inquantifiable changes to the flow of current around the electrodes andinfluence the magnitude and characteristics of the signal measured insuch a CReMS.

In embodiments, the biosensor detects a change a global phenotype withevent specificity. A global phenotype comprises one or more cellularresponse parameters selected from the group consisting of pH, celladhesion, cell attachment pattern, cell proliferation, cell signaling,cell survival, cell density, cell size, cell shape, cell polarity, O₂,CO₂, glucose, and combinations thereof. With respect to eventspecificity, a cellular parameter is selected that reflects a change ina cell sample that is an expected change for that type of therapeuticand/or activator agent. For example, if a therapeutic agent is known totarget a cytoskeletal element, a cell contacted with such an agent wouldbe expected to show a change in cell adhesion in the presence of theagent.

In some embodiments, the change in attachment pattern is a change incell adhesion. In some cases, the change in cell adhesion is indicatedby a change in a refractive index or a change in impedance. In yet otherembodiments, the change in attachment pattern is a change in basalmorphology, a change in cell density, or a change in cell size or cellshape. In a specific embodiment, the change in basal morphology is achange in cell polarity. In embodiments, a decrease in cell signalingindicates a change in cytoskeletal organization.

In embodiments, the methods of the disclosure provide for analysis ofcell samples that are label free and that can be measured in real time.In embodiments, the cell sample analyzed is a label free, viable, andnot subject to any treatments to fix the cells. In embodiments,therapeutic and/or activator agents used in the methods and kits of thedisclosure are also label free. To date label free methods have not beenapplied to determining therapeutic efficacy in effective ways.

Label free assays can reduce the time and cost of screening campaigns byreducing the time and misleading complications of label assays. Assaysthat can identify and quantify gene expression, gene mutation, andprotein function are performed in formats that enable large-scaleparallelism. Tens-of-thousands to millions of protein-protein or DNA-DNAinteractions may be performed simultaneously more economically withlabel-free assays.

In contrast to the large variety of labeled methods, there arerelatively few methods that allow detection of molecular interaction andeven fewer still for cellular function without labels. Label-freedetection removes experimental uncertainty created by the effect of thelabel on molecular folding od therapeutic and activator agents, blockingof active sites on cells, or the inability to find an appropriate labelthat functions equivalently for all molecules in an experiment that canbe placed effectively within a cell. Label-free detection methodsgreatly simplify the time and effort required for assay development,while removing experimental artifacts from quenching, shelf life, andbackground interference.

Although labels are a mainstay of biochemical and cell-based assays,there are disadvantages to their use. Labels comprise the majority ofall assay methods and have to overcome several problems, especially inthe context of the study of complex activities in human cells. Use ofradioactive labels create large quantities of contaminated materials andmust be used in specialized facilities with regulatory methods toprevent harm (at the cellular level) to those that use them. Theexcitation/emission efficiency of fluorophores is degraded by time andexposure to light, reducing the ability of the label to be accurate andprecise, and requiring that assays be read once only in an end pointmanner so that temporal information cannot be obtained. All label-basedassays require a significant amount of time to develop a process forattaching the label in a homogenous and uniform manner, determining thatthe label will be linearly quantitative, and will not interfere oraffect the interaction or process being measured. The uniformapplication of labels in complex mixtures is complicated by the presenceof all the molecules that are needed for the process to proceednaturally. Addition of the label only allows for visualization of thatmolecule function indirectly, not the entire system function directly(i.e. some extended assumptions may be necessary). Cellular activitiesare even more difficult to measure accurately with labels. Besidesfiguring out how the label will get onto the right molecule, the rightway, in the right location with respect to the cell, it is presentlyimpossible to be certain that the label is not disturbing the normalcellular processes, thereby making the extrapolation to in vivoconditions tenuous.

Label-free detection generally involves the use of a transducer that iscapable of directly measuring some physical property of a biologicalcompound or bioentity such as a DNA molecule, peptide, protein, or cell.All biochemical molecules and cells have finite physical values forvolume, mass, viscoelasticity, dielectric permittivity, heat capacityand conductivity that can be used to indicate their presence or absence,increase or decrease, and modification using a type of sensor.Additionally living systems utilize molecules to provide energy andcarry out their life processes, such as O₂/CO₂ consumption/generation,glucose production/consumption, ATP production/consumption that causemeasurable changes such as pH in their environ over finite periods oftime. The sensor functions as a transducer that can convert one of thesephysical properties into a quantifiable signal such as a current orvoltage that can be measured.

In some cases, in order to use a transducer as a bio sensor, the surfaceof the transducer must have the ability to selectively capture specificmaterial such as a protein or specific cell type, while not allowingundesired material to attach. Selective detection capability is providedby building of a specific coating layer of chemical molecules on thesurface of the transducer. The material that is attached to the sensorsurface is referred to as the sensor coating while the detected materialis called the analyte. Thus, in some cases, a biosensor is thecombination of a transducer that can generate a measurable signal frommaterial that attaches to the transducer, and a specific recognitionsurface coating containing a receptor ligand that can bind a targetedanalyte from a test sample.

In embodiments, a coating is selected for a biosensor that is associatedwith a particular cellular component or pathway. For example, in thosecases, where the cellular physiological parameter is change in celladhesion, a coating is selected that provides for adhesion of the cellsin the cell sample to the biosensor surface. In embodiments, the coatingthat enhances adhesion of the cells to the biosensor includesextracellular matrix, fibronectin, integrins and the like. In otherembodiments, a coating is selected that binds to a particular cell typebased on a cell surface marker. In embodiments, such cell surfacemarkers include, CD20, CD30, EGFR, EGFR-TK, PI3K, MEK1, MEK2, HER2receptor, Her3 receptor, Her4 receptor, VEGFR, and other cell surfacecancer biomarkers.

In embodiments, the biosensor is coated with a biomolecular coating.CReMS surfaces contacting cells may contain a biomolecular coating priorto addition of cells, during addition of cells, or after addition ofcells. The coating material may be synthetic, natural, animal derived,mammalian, or created by cells placed on the sensor. For example, abiomolecular coating can comprise an extracellular matrix componentknown to engage integrins, adherins, cadherins and other cellularadhesion molecules and cell surface proteins (e.g., fibronectin,laminin, vitronectin, collagens, IntercellularCAMs, VascularCAMs,MAdCAMs), or a derivative thereof, or can comprise a biochemical such aspolylysine or polyornithine, which are polymeric molecules based on thenaturally occurring biochemicals lysine and ornithine, polymericmolecules based on naturally occurring biochemicals such as amino acidscan use isomers or enantiomers of the naturally-occurring biochemical,antibodies, fragments or peptide derivatives of antibodies, complementdetermining region (CDR), designed to attach specific cell surfaceproteins to the biosensor,

A biosensor comprises an area to seed cells. For example, a biosensorcan comprise a microtiter plate containing wells to seed cells. One ormore cell samples can be seeded on a biosensor by physical adsorption toa surface in a distinct location. A biosensor can comprise 1, 10, 24,48, 96, 384, or more distinct locations. A cell sample can compriseabout 100 to about 100,000 individual cells or any cell number inbetween. An optimal cell sample depends on the size and nature of adistinct location on a biosensor. A cell sample can comprise about 5000cells or less; about 10,000 cells or less; about 15,000 cells or less;about 20,000 cells or less; about 25,000 cells or less; or about 50,000cells or less. A cell sample can comprise about 1000 to about 2500cells; about 1000 to about 5000 cells; 5000 to about 10,000 cells; about5000 to about 15,000 cells; about 5000 to about 25,000 cells; about 1000to about 10,000 cells; about 1000 to about 50,000 cells; and about 5000to about 50,000 cells.

In embodiments, a change in a cellular response or physiologicalparameter is measured over a defined period of time. In embodiments, thedefined period of time is the amount of time that it takes for thecontrol cells to reach a steady state in which a change in the output ofthe physiological parameter varies by 20% or less. In embodiments, thechange is observed in cells in 1 hour or less. In other embodiments, thechange is observed in cells for at least 1 min. to about 60 min. andevery minute in between. In other embodiments, the change in cellresponse is measured from about 10 minutes to about one week or 200hours. In embodiments, when a therapeutic agent is targeted to acellular pathway, the cellular response is measured from about 10minutes to about 5 hours, about 10 minutes to about 4 hours, about 10minutes to about 3 hours, about 10 minutes to about 2 hours, about 10minutes to about 1 hour, or about 10 minutes to about 30 minutes or anytime point in between. In embodiments, when a therapeutic agent affectscell proliferation or cell killing or cellular resistance, the cellularresponse is measured from about 1 hour to about 200 hours. In yet otherembodiments, a combination of responses (otherwise described as a fulltemporal pattern) between 1 minute and 200 hours is used to determinetherapeutic effect of a compound on cells and the cells ability todevelop resistance. This timeframe encompasses the important process ofshort-term pathway signaling, dynamic reprogramming and longer termcellular responses important in assessing a probable response andmaintenance thereof in a patient.

Once cells of a particular subject have been seeded on a biosensor,baseline measurements can be determined. Baseline measurements can betaken on the same cell sample, or a control cell sample. A controlsample can comprise healthy cells or diseased cells from the samepatient and/or same tissue. A control sample can comprise disease cellsknown to respond to the agent. In other embodiments, a control samplecomprises disease cells known not to respond to the agent. A controlsample may include application of an activator agent to healthy ordiseased cells of a particular patient, designed to elicit astandardized response relating to cell health, cell metabolism, or cellpathway activity.

The control would be determined for each disease and or drug type. Onepractice would be a comparison against a healthy cell control from thesame patient. For example, with cell killing drugs, the method will showbenefit of killing disease cells over healthy cells to achieve asignificant therapeutic index. Other ideal embodiments would include theuse of pathway tools to determine pathway function and control by thedrug. In an example of targeted therapeutics, tools are activatoragents, bioreagents or small molecules used as controls to perturb apathway and determine a targeted drug's ability to disrupt theperturbation. For yet other embodiments, the physiologic effect of adrug on cell would be measured without exogenous perturbation by anactivator agent noting for example the temporal pattern or rate ofoxygen consumption, the rate or temporal pattern of acidification, ionflux, or metabolite turnover.

A continuous time course of the biosensor signal is the preferredembodiment. There are distinctive patterns on the time vs. biosensorsignal plot that are indicative of a patient cell response to drugtreatment. Evaluation of these patterns is useful to identify thepresence of an efficacious event. A time course or constantly changingmeasurement of live and fully functional cells is more beneficial thanthe current practice used in typical whole cell assays that onlyrepresent a point in time. The methods described herein measure dynamicsystems as they would occur in a patient and represent the most accuratemeans of determining patient response. In the case of pathway responses,recording of a complete time course or temporal pattern is superior inability to support more complex analysis and obviates selecting theoptimum time point for a single measurement.

Comparison against controls could occur at a temporal maxima, minima, oras differences between maximal signal-minimal signal, or by comparingintegrated areas under a curve (AUC) for a time course plot or othernon-linear comparisons of the test well against positive or negativecontrol wells. Additional analyses supported only by measuring with abiosensor are time to reach maxima/minima, and other derivatives of thetemporal time course. In the case of longer term responses, the time ofcomparison may be of a specific time point after a few days or a week oftreatment or multiple applications of drug. The longer time course mayalso compare changes in slope or compare second derivatives of the timeversus biosensor signal plot at the beginning, middle or end of a weekof drug treatment. Significant changes compared to control may includeabsolute drop in biosensor signal related to curtailment of cellularmetabolism. Alternatively, the drop may be followed by an increase thatcould indicate development of resistance to the drug during the assay.Additionally, non-linear Euclidean analyses could be used to produce ameasure of total differences between controls and patient samples over acomplete time-course. This too would be significant with respect topredicting the outcome for a patient.

In embodiments, the output of a biosensor over a defined period of timeis represented as a cell index. The cell index is the change inimpedance from a test starting point. Cell Index is defined as ameasurement of impedance and can be applied in one instance of thepresent invention by measuring at a fixed electrical frequency of, forexample, 10 kHz and fixed voltage.

And calculated by the equation Cell Index_(i)=(R_(tn)−R_(t0))/F

Where:

i=1, 2, or 3 time point

F=15 ohm in one example when the instrument is operated at 10 kHzfrequency

R_(t0) is the background resistance measured at time point T0.

R_(tn) is the resistance measured at a time point Tn following celladdition, cell physiologic change, or cell perturbation.

Cell index is a dimensionless parameter derived as a relative change inmeasured electrical impedance to represent cell status. When cells arenot present or are not well-adhered on the electrodes, the CI is zero.Under the same physiological conditions, when more cells are attached onthe electrodes, the CI values are larger. CI is therefore a quantitativemeasure of cell number present in a well. Additionally, change in a cellphysiological status, for example cell morphology, cell adhesion, orcell viability will lead to a changes in CI.

The cell index is a quantitative measure of the presence, density,attachment or changes thereof based upon a starting point or baselineimpedance measurement. The baseline starting point impedance is aphysical observable characteristic and an indication of the health,viability, and physiologic status of a cell prior to any treatment withdrug or other perturbant. The baseline starting point can be used as aqualitative control for the CELx test. Addition of drug or perturbantcauses the impedance to change in temporal patterns reflective of thespecificity of the cellular physiologic change experienced by the cell.Changes in a cell physiological status, for example cell morphology,cell number, cell density, cell adhesion, or cell viability will lead toa changes in the cell index.

A change in a cellular response or physiological parameter is determinedby comparison to a baseline measurement. The change in cellularparameter or physiological response depends on the type of CReMS. Forexample, if the change in cellular response is determined optically,physically observable changes could be measured for example as afunction of optical density at spectral wavelengths for chemicalabsorbance or transmittance, changes in a surface plasmon measurementdevice, or changes detected by photonic crystal devices. If the changein cellular parameter or physiological response is determinedelectrically, physically observable changes could be measured forexample using milli or micro impedance changes of cells adhered toelectrodes. Changes in pH, glucose, carbon dioxide, or ions, could bemeasured electronically using ion selective field effect transistors(ISFET).

In other embodiments, a rate of change is determined by a methodmeasuring a CReMS response for a period of time required to determine adifference in cellular physiologic response to a therapeutic. The rateof change is described by various interpretation of the time course dataand can be expressed as a rate or further derivative function of therate including acceleration of the rate.

In embodiments, one or more cutoff values for determining a change incellular response is determined by a method comprising: determining astandard deviation, a signal to noise ratio, a standard error, analysisof variance, or other statistical test values known by those practicedin the art for determining appropriate confidence intervals forstatistical significance of a set of samples from known responding cellsamples and from a set of samples from known nonrespondingpatiecompunts; and determining the difference between the two andsetting the cutoff value between the confidence intervals for bothgroups. Preferred embodiments include 80-90% confidence intervals, morepreferred embodiments include >90% confidence intervals and mostpreferred embodiments include >95% or >99% confidence intervals. Inembodiments, a cutoff value is validated by determining the status ofblinded known samples as responders or nonresponders using a cutoffvalue and unblinding the sample and determining the accuracy ofpredicting the status of the sample. In the case of a single cutoffvalue, values that fall below the cutoff value or are closer to thevalues for the known responders indicate the patient sample isexhibiting responsiveness to the therapeutic agent and if the values areat or above the cutoff value or are closer to the values for the knownnon responders value, the cell sample is identified as a non responderto the therapeutic agent.

In some embodiments an output of the biosensor at a defined period oftime is classified as no response, weakly responsive or responsive. Anoutput at a defined period of time is selected in order to classify theoutput into the categories. In embodiments, the defined period of timeis the end point of the time period for which the cells have beencontinuously monitored in the biosensor. In embodiments, the time periodis at least 60 minutes, 60 hours, or 120 hours. In embodiments, anoutput classified as no response, is indicated by an output value thatdiffers from the output value of the baseline prior to administration ofa therapeutic agent or a control cell not treated with the therapeuticagent no more than at least 20% or less, 15% or less, 10% or less, or 5%or less. In embodiments, an output classified as weakly responsive isindicated by an output value that differs from the output value of thebaseline prior to administration of a therapeutic agent or a controlcell not treated with the therapeutic agent of at least 50% or less andgreater than 5%. In embodiments, an output classified as responsive isindicated by an output value that differs from the baseline prior toadministration of a therapeutic agent or a control cell not treated withthe therapeutic agent of at least greater than 50%. In embodiments, thecontrol sample is a sample of the disease cells from the same subjectand not treated with the therapeutic agent.

Therapeutic and Activator Agents

Often a when a patient is diagnosed with a particular disease orcondition, there is a range of treatment options. In some cases,treatments may be very expensive or the side effects associated with thetreatment may be severe so it would be useful to know whether thepatient is likely to be a responder or a non-responder to a treatment.In addition, if a patient becomes resistant, it would be useful to knowwhich other treatments might be efficacious now that the patient'sdiseased cells have become resistant.

In embodiments, any therapeutic agent or agents that are used in thetreatment of a condition for which some patients respond and others donot respond can be analyzed in the methods described herein. Forexample, for cancer, a number of targeted immunotherapies are availableincluding a number of different chimeric and humanized antibodies. Forautoimmune conditions, molecules such as those targeted to inflammatorycytokines or their receptors may be analyzed. Examples of agentstargeted to inflammatory cytokines are anti-TNF a agents, agentstargeting interferon alpha, interleukins, and the like.Immunosuppressive agents such as corticosteroids, tacrolimus (FK-506 orTACR) (inhibits T-cell metabolism and proliferation), sirolimus(SIRO/81768), myocophenolic acids, mycophenolate mofetil (MMF),calcineurin inhibitors (CI), cyclosporin (CsA), and rapamycin (mTORinhibitor).

In embodiments, the methods as disclosed herein involve testing of oneor more therapeutic agents for the ability to cause a change in aphysiological parameter of the diseased cells from the individualsubject. In embodiments, the therapeutic agents are also label free. Insome embodiments, two or more therapeutic agents may be testedseparately or in combination on separate samples of the diseased cellsfrom the same patient. A therapeutic agent is selected that causes thegreatest change in the cellular response or physiological characteristicat a lower dose than other therapeutic agents. Combinations of compoundsmay be determined that offer the greatest therapeutic effect. Inembodiments, the determination may be as compared to healthy cells ofthe patient to determine therapeutic index and other individual safetyand tolerance effects.

In some embodiments, when a therapeutic agent is a targeted therapeuticagent that affects a cellular pathway, the change in cellularresponsiveness is measured in the absence or presence of an activatoragent or perturbant of the pathway. A therapeutic agent is selected thatinhibits the cellular responsiveness to the perturbant of the pathway ascompared to baseline measurement and optionally, as compared to othertherapeutic agents.

In other embodiments, when a therapeutic agent is a targeted therapeuticagent that binds to a cell surface receptor, the change in cellularresponsiveness is measured in the absence or presence of an activatoragent or perturbant that binds to the receptor. In embodiments, thetherapeutic agent is administered to the cell sample before or after theactivator or perturbant. In embodiments, the activator agent orperturbant is label free. A therapeutic agent is selected that inhibitsthe cellular responsiveness to the activator agent or perturbant ascompared to baseline measurement and optionally, as compared to othertherapeutic agents, regardless of the density of the cell surfacereceptors. In some embodiments, a therapeutic agent is selected thatinhibits the action of the activator agent or perturbant independent ofthe density of cell receptors. The change in the physiological parametercan be an increase or a decrease in the parameter as compared tobaseline or healthy cell control. The changes could represent fullagonism, superagonism, irreversible agonism, selective agonism,co-agonism, inverse agonism, or partial limiting agonism, reversible andirreversible antagonism, competitive antagonism, non-competitiveantagonism, un-competitive antagonism. The changes can occur sooner,later or not at all as compared to an appropriate control. The changescould be selected to occur for a longer or shorter period of time.Changes could be selected that are reversible or irreversible.

For example, a therapeutic agent that results in a decrease in cellsignaling would be selected for treatment of an autoimmune condition.Peripheral blood cells that respond to an agent that inhibits the actionof a cytokine show a decrease in cell signaling. In another example, fordisease cells responsive to an anticancer agent, such as a humanizedantibody targeted to a receptor like Her2, the disease cells would showa significant reduction in EGF family pathway signaling. In other cases,for disease cells responsive to an anti-angiogenic agent, the diseasecells would show a reduction in VEGF pathway signaling or reduction inproliferative ability. The CReMS response or physically observablecharacteristic measured for each type of agent is dependent upon theintended physiological response the drug was designed to illicit and canbe as specific or general as needed. The key is the use of the CReMS forphysiological measurement of a live cell for a period of time to testthe response the drug was intended to alter.

A particular therapeutic agent or agents can be administered to thediseased cells, and optionally, healthy cells to determine theeffectiveness of the particular therapeutic or therapeutics. Diseasedcells and/or healthy cells can also be untreated so as to compare theeffect of the therapeutic or therapeutics on treated and untreateddiseased and/or healthy cells. A single therapeutic can be administeredto determine how a subject will respond to the therapeutic treatment. Inanother embodiment, a panel of different therapeutics can beadministered to cells of a particular subject.

In embodiments, a cutoff value for efficacy of a therapeutic agent toinhibit activation of a cellular pathway is determined in one embodimentby adding the drug and measuring the physiologic response. In anotherembodiment, the pathway is stimulated with and without drugpre-treatment. Changes to the physiologic baseline signal or reductionsof the stimulation signal by the drug at the 85% confidence interval orideally greater than the 90% confidence interval or more ideally greaterthan the 95% or 99% confidence interval are deemed efficacious. Inembodiments, a cutoff value for efficacy of a therapeutic agent thatinhibits cell proliferation or enhances cell killing is determined byrecording the physiologic response over time. Reductions to thephysiologic baseline signal or deviation from the temporal pattern ascompared to non-treated or healthy cells or a combination thereof by thedrug at the 85% confidence interval or ideally greater than the 90%confidence interval or more ideally greater than the 95% or 99%confidence interval are deemed efficacious.

The sensitivity and specificity of the therapeutic agent for treatingthe disease of an individual subject is determined by comparing thecellular physiologic pathway response as measured by the CReMS todetermine that the drug is working as it was designed on a specifictarget and determining that a cutoff value for efficacy has beenattained.

Therapeutic agents can include without limitations agents that aretargeted to a particular cellular pathway and/or agents that inhibitcell proliferation or cause cell killing. Examples of pathways thattherapeutic agents target include MAPK-PK, RAS/RAF, RHO, FAK1, MEK/MAPK,MAK, MKK, AKT, EGF receptor, Her2 receptor, Her 3 receptor, Her 4receptor, PIK3/PTEN, VEGF receptor pathway inhibitors, cell adhesion,TGFbeta/SMAD, WNT, Hedgehog/GLI, HIF1 alpha, JAK/STAT, Notch, control ofG1/S transition, DNA damage control, apoptosis

In embodiments, therapeutic agents comprise a number of small moleculeand antibody drugs such as trastuzumab, pertuzumab, lapatinib,docetaxel, tamoxifen, cisplatin, abraxane, paclitaxel injection,brentuximab vedoton, everolimus, pemetrexed, exemestane, ofatumumab,bevacizumab, alemtuzumab, irinotecan, bicalutamide, oxaliplatin,cetuximab, visomedegib, toremifene citrate, fulvestrant, gemcitabine,imatinib, ixabepilone, topeotecan, axitinib, romidepsin, cabrazitaxel,sorafenib, infliximab, lenalidomide, rituximab, dasatinib, sunitinib,erlotinib, nilotinib, paclitaxel, temozolomide, trioxide, panitumumab,bortezomib, azacitidine, pazopanib, crizotinib, capecitabine,ipilimumab, vemurafenib, goserelin acetate, abiraterone, a BH3 mimetic,navitoclax, anastrozole, letrozole, an aromatase inhibitor,cyclophosphamide, doxorubicin, methotrexate, fluorouracil, ixabepilone,carboplatin, aflibercept, temsirolimus, irbritumomab, abiraterone,custirsen, neratinib and combinations thereof. The targets of thesetherapeutic agents are known.

In embodiments, a method for determining therapeutic efficacy of anagent for a disease in an individual subject comprising: administeringthe agent to at least one isolated disease cell sample from theindividual subject in a cellular response measurement system (CReMS);and determining whether a change in a cellular response parameter of thecell sample to the agent occurs as compared to a baseline measurement,wherein the change in cellular response indicates that the agent hastherapeutic efficacy for the disease in the individual subject. Inembodiments, a method further comprises administering to at least oneisolated disease cell sample from the individual subject in a cellularresponse measurement system an activator agent or perturbant thatperturbs the cellular response pathway before or after administering thetherapeutic agent.

In some embodiments, the therapeutic agent is targeted to a cell surfacereceptor and/or a cellular pathway. In that case, the sample iscontacted with a therapeutic agent before the sample is activated withan activator agent or perturbant of the pathway. In embodiments, theactivator agent or perturbant comprises a specific growth factor,vascular endothelial growth factors, phosphatidyl inositol, epidermalgrowth factors, hepatocyte growth factors, m-CSF, RANK ligand, TumorNecrosis Factors (TNF-α), neuregulin, estrogen, progesterone, folate,adenosine triphosphate, and FAS Ligand, Platelet derived growth factors(PDGF), or other agents of cellular pathway or signaling stimulationsuch as the subject's plasma or serum, Na+, K+, Mg+, Cl—, Ca+2, glucose,glutamine, histidine, mannitol, and tryptophan, antibiotics (rapamycin),essential and non-essential amino acids, vitamins, other organiccompounds, trace minerals and inorganic salts, serum, cell extracts,fractionated cell extracts or fractionated serum, extracellularsignaling factors, intracellular signaling factors, insulin,transferrin, sodium selenite, hydrocortisone, ethanolamine,phosphophorylethanoloamine, tridothyronine, sodium pyruvate,L-glutamine. In embodiments, therapeutic agents are those that affectdiseased cells by inhibiting cell proliferation, enhancing cell killing,and rendering the cell unresponsive or less responsive to signals thatlead to a diseased state. Examples of such therapeutic agents includecyclophosphamide, 5-FU, capaecitabine, and other pyrimidine drugs,others SN-38 metabolite analogs (Ex. irinotecan), taxols, and platinumcontaining drugs (Ex. cisplatin).

In some embodiments, the response of a sample to one or more of theseagents can also be measured in the presence or absence of a growthfactor that stimulates cell proliferation or of an anti-apoptotic agent.Growth factors that stimulate cell proliferation include growth hormone,epidermal growth factor, vascular endothelial growth factor, plateletderived growth factor, hepatocyte growth factor, transforming growthfactor, fibroblast growth factor, nerve growth factors, and others knownto those practiced in the art. Anti-apoptotic agents include compoundsthat regulate anti-apoptotic proteins or pathways (Ex. taxols on Bcl-2protein activity and Gefitinib for control of the anti-apoptotic Rassignalling cascade).

For example, for a particular subject diagnosed with breast cancer anddetermined to be Her2 positive, cells isolated from that subject can betested for responsiveness to particular anti-cancer therapeutics,especially anti-Her2 therapeutics. For instance, cells from the Her2+subject can be tested for responsiveness to trastuzumab or lapatinib inthe presence or absence of epidermal growth factor (EGF) and/orhomologous structured peptides, neuregulin, or heregulin. In anembodiment, cells from the subject can be seeded on a biosensor. Inembodiments, cells are label free whole cells. Such cells can be bothcells from the breast cancer tumor and healthy breast tissue.Trastuzumab or lapatinib can be administered to a sample of diseasedcells and, optionally, a sample of healthy cells. In some embodiments,the cell samples treated with trastuzumab are then contacted with Herreceptor activator such as neuregulin. A sample of both diseased andhealthy cells can remain untreated. A cellular response is determinedusing a cellular response measurement system (CReMS). In embodiments,the cellular response is determined after 1 hour or less. Theeffectiveness of trastuzumab treating the cells of the particularsubject can then be determined in the presence or absence ofperturbation of the pathway.

In embodiments, an agent is selected that inhibits the cellular responseof the individual subject's cell sample to an activator of the cellularpathway, activator of cell proliferation, or inhibitor of apoptosis.When a number of different therapeutic agents that activate the same ordifferent pathways are evaluated in a method of the disclosure, an agentis preferably selected that can inhibit the activator or inhibitorresponse at a lower concentration than the others.

In similar embodiments, therapeutic agents are those that affectdiseased cells by agonizing or partially agonizing cellular activitywhere reduced activity has led to the diseased state.

The test can measure the effectiveness of a drug in a range ofconcentrations from below 1 nM to greater than 100 uM generally withless than 20% standard deviation and optimally with less than 5%standard deviation. The compound test range will correspond to dosinglevels as defined on a drug packaging label known as the maximumtolerated dose. Unlike most tests that cannot ascertain the number oflive cells in the actual set of cells in the test, this test is onlyworking with the live cells as determined in a quality control andbaseline physiologic determination step at the beginning of the test.The result of this feature reduces the variance of the test result. Thetest can be conducted using a temperature, oxygen, humidity, and carbondioxide range generally acceptable for cell viability commonly known tothose practiced in the art. In some cases, a preferred temperature rangeis between 25° C.-40° C. In other cases the temperature may be optimizedfurther to +0.5° C. within this range for specific perturbations andmaintained using standard temperature controlled incubator cabinets.

In another embodiment, samples of the diseased cells form an individualcan be tested for responsiveness to a panel of anticancer therapeutics.For cancer, a number of small molecule and antibody drugs are available.Examples of such therapeutic agents include trastuzumab, pertuzumab,lapatinib, docetaxel, tamoxifen, cisplatin, abraxane, paclitaxelinjection, brentuximab vedoton, everolimus, pemetrexed, exemestane,ofatumumab, bevacizumab, alemtuzumab, irinotecan, bicalutamide,oxaliplatin, cetuximab, visomedegib, toremifene citrate, fulvestrant,gemcitabine, imatinib, topeotecan, axitinib, romidepsin, cabrazitaxel,sorafenib, infliximab, lenalidomide, rituximab, dasatinib, sunitinib,erlotinib, nilotinib, paclitaxel, temozolomide, trioxide, panitumumab,bortezomib, azacitidine, pazopanib, crizotinib, capecitabine,ipilimumab, vemurafenib, goserelin acetate, abiraterone, a BH3 mimetic,navitoclax, anastrozole, letrozole, an aromatase inhibitor,cyclophosphamide, doxorubicin, methotrexate, fluorouracil, andcombinations thereof.

For instance, samples of cells collected from a Her2+ subject can testedagainst a panel of anti-breast cancer therapeutics, including anti-Her2therapeutics. In an embodiment, each sample of cells from the subjectcan be administered one of the anti-breast cancer therapeutics. A panelof anti-breast cancer therapeutics can include, but are not limited to,trastuzumab, pertuzumab, lapatinib, docetaxel, tamoxifen, cisplatin, aBH3 mimetic, an aromatase inhibitor, cyclophosphamide, doxorubicin,methotrexate, fluorouracil, NeuVax™ (E75 peptide administered withadjuvant sargramostim (rGM-CSF)), and combinations thereof. Thearomatase inhibitor can be at least one of aromatase inhibitor isanastrozole, letrozole, or exemestane. The BH3 mimetic can benavitoclax.

In an embodiment, an anti-breast cancer therapeutic can be a Her/Neureceptor family activity modulators (e.g., pertuzumab), cellular growthfactor receptor modulators (e.g., modulators of vascular endothelialgrowth factor (VEGF) receptors), mitogen activated protein kinase (MAPK)pathway modulators, (PI3K) pathway modulators, a BH3 mimetic, anaromatase inhibitor, or combinations thereof.

Methods of the invention include administering candidate therapeutics toa subject's cells to determine safety and to determine therapeuticeffectiveness. Additionally, administration of a candidate therapeuticto a subject's diseased cells may be used as a method of selecting theproper patient population for a phase II or III clinical trial. Methodsof the invention include testing diseased cells against knowntherapeutic combinations. Additionally, methods of the invention includetesting known and candidate therapeutics.

Methods of the invention also including administering combinations oftherapeutic agents to determine if a particular combination of agentsproduces a more effective result (i.e., amelioration or cure of diseasesymptoms). A combination of therapeutic agents is two or moretherapeutic agents administered to the same cell sample. In anembodiment of the invention, the combination of therapeutic agents isadministered to a cell sample concurrently. In an embodiment, at leastone therapeutic agent is administered to the cell sample at a timedifferent than the administration of the other at least one therapeuticagent of the combination.

After administration of therapeutic agents to a cell sample, real timedata can be collected on multiple aspects of the cell sample. Forinstance, pH and temperature can be measured. Additionally, otherfactors, such as “cell death factors”, can be determined. A cell deathfactor as determined by a CReMS can be a change in a physicochemicalproperty as measured by the CReMS. For instance, cancer cells willattach to a surface and provide a baseline reading for a refractiveindex. Administration of a therapeutic agent that promotes cancer celldeath would cause a change in the refractive index since the cancercells in a sample would round up and detach from a surface. This couldbe measured by an optical biosensor utilizing surface plasmon resonancein a continuous real-time manner.

An embodiment includes a method for determining therapeutic efficacy ofan agent for a particular subject comprising administering the agent toa disease cell sample from the subject in a CReMS and determining thephysiologic response of the cell sample to the agent compared to abaseline measurement, wherein the physiologic response indicatestherapeutic efficacy of the agent. The agent administered to a diseasecell sample can be a single agent or two or more agents. When the agentis two or more agents, the two or more agents can be administeredconcurrently or at different times. For instance, one agent can beadministered to a cell sample and a second agent can be administered alater time (e.g., 10 minutes later). A method can also includeadministering a placebo to a diseased cell sample. A method can alsoinclude administering the agent(s) to be tested on a healthy cellsample.

In embodiments, the methods as described herein provide for a method todetermine an optimal dose range for a particular therapeutic.Determination of a dose range allows for proper design of clinicaltrials and/or allows the physician to balance efficacy with detrimentalside effects. In embodiments, a method comprises administering a rangeof doses of a therapeutic agent to separate samples of diseased cellsfrom the same patient, and determining the dose range that results in achange in a physiological parameter of the cells as described herein ascompared to baseline and/or healthy control cells.

Once any of the methods described herein are used to determine whetheran individual subject's disease cells respond to one or more therapeuticagents, the results are communicated to a health care worker to allowfor selection of a therapeutic agent for treatment of the subject. Inembodiments, the methods further comprise administering the selectedtherapeutic agent to the subject.

Kits

In another aspect of the disclosure kits are provided. In embodiments akit comprises a container for a disease cell sample from an individualsubject containing a transport medium; a container for a control cellsample from the individual subject containing a transport medium; abiosensor; a non transitory computer readable medium having computerexecutable instructions for converting data from the biosensor into anoutput, wherein the output shows a change in a cellular physiologicalresponse parameter over a defined period of time, wherein the cellularphysiological response parameter is selected from the group consistingof pH, cell adhesion, cell attachment pattern, cell proliferation, cellsignaling, cell survival, cell density, cell size, cell shape, cellpolarity, O₂, CO₂, glucose, and combinations thereof; classifying theoutput as above or below a cutoff value indicating status as a responderor nonresponder and/or classifying the sample as having no response,weakly responsive, and responsive; and generating a report with theclassification.

Types and amount of a disease cell samples are described herein. Inembodiments, the disease cell sample is a whole cell label free viablecell sample having at least 5,000 cells. In embodiments, a control cellsample is selected from the group consisting of a disease cell samplefrom the same subject, a healthy cell sample from the same subject, acell sample known to respond to the therapeutic agent, a cell sampleknown not to respond to the therapeutic agent, and combinations thereof.

The containers and the transport medium are designed to maintain cellviability and to minimize cell activation. In embodiments, the media andcontainers are endotoxin free, nonpyrogenic and DNase- and RNase-free.Once obtained the cell samples are maintained in a transport medium thatretains the cell viability. Depending on the length of time fortransportation to the site of analysis, different media may be employed.In embodiments, when transportation of the tissue sample may require upto 10 hours, the media has an osmolality of less than 400 mosm/L andcomprises Na+, K+, Mg+, Cl—, Ca+2, glucose, glutamine, histidine,mannitol, and tryptophan, penicillin, streptomycin, contains essentialamino acids and may additionally contain non-essential amino acids,vitamins, other organic compounds, trace minerals and inorganic salts,serum, cell extracts, or growth factors, insulin, transferrin, sodiumselenite, hydrocortisone, ethanolamine, phosphophorylethanoloamine,tridothyronine, sodium pyruvate, L-glutamine, to support theproliferation and plating efficiency of human primary cells. Examples ofsuch a media include Celsior media, Roswell Park Memorial Institutemedium (RPMI), Hanks Buffered Saline, and McCoy's 5A, Eagle's EssentialMinimal Media (EMEM), Dulbecco's modified Eagle's medium (DMEM),Leibovitz L-15, or modifications thereof for the practice of primarycell care.

Biosensors are described herein. In embodiments a biosensor is selectedfrom the group consisting of a biosensor that detects a cellularparameter selected from the group consisting of, cell adhesion, cellattachment, cell morphology, cell phenotype, cell proliferation, cellsignaling, cell density, cell polarity, pH, O₂, CO₂, glucose, andcombinations thereof. In embodiments, the device is an impedance or anoptical device. Biosensors may be optionally coated as described herein.In embodiments, a biosensor is selected that measures a change in aphysiological parameter associated with the type of therapeutic and/oractivator agent as described herein.

In embodiments a kit comprises a non-transitory computer readable mediumhaving computer executable instructions for converting data from thebiosensor into an output, wherein the output shows a change in acellular physiological response parameter over a defined period of time,wherein the cellular physiological response parameter is selected fromthe group consisting of pH, cell adhesion, cell attachment pattern, cellproliferation, cell signaling, cell survival, cell density, cell size,cell shape, cell polarity, O₂, CO₂, glucose, and combinations thereof;classifying the output as a responder or nonresponder and/or noresponse, weakly responsive, and responsive; and generating a reportwith the classification.

In embodiments, the disclosure provides a computing device or computerreadable medium with instructions to implement the methods of thedisclosure. The computer readable medium includes non-transitory CD,DVD, flash drive, external hard drive, and mobile device.

The kits and methods described herein can employ the use of aprocessor/computer system. For example, a general purpose computersystem comprising a processor coupled to program memory storing computerprogram code to implement the method, to working memory, and tointerfaces such as a conventional computer screen, keyboard, mouse, andprinter, as well as other interfaces, such as a network interface, andsoftware interfaces including a database interface find use oneembodiment described herein.

The computer system accepts user input from a data input device, such asa keyboard, input data file, or network interface, or another system,such as the system interpreting, for example, the data generated by thebiosensor over a defined period of time, and provides an output to anoutput device such as a printer, display, network interface, or datastorage device. Input device, for example a network interface, receivesan input comprising a change in a cellular physiological parameter asdescribed herein and/or quantification of these changes. The outputdevice provides an output such as a display, including one or morenumbers and/or a graph depicting the detection and/or quantification ofthe change in a cellular parameter.

Computer system is coupled to a data store which stores data generatedby the methods described herein. This data is stored for eachmeasurement and/or each subject; optionally a plurality of sets of eachof these data types is stored corresponding to each subject. One or morecomputers/processors may be used, for example, as a separate machine,for example, coupled to computer system over a network, or may comprisea separate or integrated program running on computer system. Whichevermethod is employed these systems receive data and provide data regardingdetection/diagnosis in return.

In some embodiments, the computing device can include a single computingdevice, such as a server computer. In other embodiments, the computingdevice can include multiple computing devices configured to communicatewith one another over a network (not shown). The computing device canstore multiple databases within memory. The databases stored on thecomputing device can be organized by clinic, practicing clinician,programmer identification code, or any other desired category.

Data from the biosensor can be sent to the remote computing system oranother data storage device. The communication process initializes andbegins at a start module and proceeds to a connect operation. Theconnect operation communicatively couples the stored information of thehealth care provider to the remote computing system, for example, via acabled connection, a wireless local area network (WLAN or Wi-Fi)connection, a cellular network, a wireless personal area network (WPAN)connection, e.g., BLUETOOTH®, or any desired communication link.

A transfer operation transmits data from the biosensor to the computingdevice. In an embodiment, the transfer operation encrypts the databefore transmitting the data between the devices. The communicationprocess can complete and end at a stop module. Once the biosensor datais transferred to a remote computing device, the data is converted to anoutput, such as a cell index measurement over time. In embodiments, adefined endpoint is selected and is used to classify the cell sample asno response, weakly responsive or responsive as described herein. Inembodiments, the status of the analysis of the sample as a responder ornon responder is communicated back to the health care provider using asimilar process over cabled connection, a wireless local area network(WLAN or Wi-Fi) connection, a cellular network, a wireless personal areanetwork (WPAN) connection, e.g., BLUETOOTH®, or any desiredcommunication link.

In embodiments, the computer readable storage medium havingcomputer-executable instructions that, when executed by a computingdevice, cause the computing device to perform steps comprising:converting data from the biosensor into an output, wherein the outputshows a change in a cellular physiological response parameter over adefined period of time, wherein the cellular physiological responseparameter is selected from the group consisting of pH, cell adhesion,cell attachment pattern, cell proliferation, cell signaling, cellsurvival, cell density, cell size, cell shape, cell polarity, O₂, CO₂,glucose, and combinations thereof in the presence and/or absence of atherapeutic agent; classifying the output as no response, and responsiveat a defined endpoint by comparing the output from biosensor from thecell sample in the presence of the therapeutic agent to the output frombiosensor from the cell sample in the absence of the therapeutic agent;and generating a report with the classification. In embodiments, thecomputer executable instructions comprise instructions for communicatingthe classification to a health care provider.

In embodiments, the computer readable storage medium may includeinstructions for identifying which pathways are operative in the diseasecell sample of the subject. The instructions that when executed by acomputing device comprise determining whether there is a differencebetween the output of the biosensor data from a disease cell sample froma subject treated with a first activating or perturbing agent to theoutput of the biosensor data from a second disease cell sample from thesame subject not treated with the first activating or perturbing agentto one another to determine whether the pathway responsive to the firstactivator or perturbant agent is active in the disease cell sample;identifying the presence of the difference in output as an indication ofactivity of the pathway, and communicating the activity of the pathwayto a health care provider. Activator or perturbant agents and theirpathways are described herein.

EXAMPLES

Discussion of Experimental Design

The methods utilize a CReMS to measure the physiologic change of a cellor cell pathway after protein binding within a cell or cell pathway hasoccurred. It is commonly understood that a drug cannot work unless it isbound, and that nearly all disease genes fall into core signalingpathways. In light of this and the fact biochemical principles ofprotein binding are universal across cell types, the methods describedherein are thus broadly applicable to all cells and cell pathways whereprotein and other biomolecule binding can occur.

The current state-of-the-art genetic tests cannot indicate directlywhether a drug or the pathway is bound, and hence they cannot reliablypredict drug response. By identifying the physiologic change that occurswithin a cell after a drug is introduced, the CELx test can reliablypredict the response of the subject's cells to the drug,

At least three types of CELx tests are envisioned using the methodsdescribed herein.

1) A Pathway Shutdown test that determines the efficacy of targetedpathway drugs. In this test, the physiologic change of the test cellscaused by the binding of a targeted pathway drug to its cellular targetis measured and compared to a baseline measurement.

2) An Anti-Proliferation test that determines the efficacy ofanti-proliferation drugs. In this test, the physiologic change of thetest cells caused by the inhibition of their proliferative capacity ismeasured and compared to a baseline measurement.

3) A Combination Test that determines the efficacy of two or more drugsutilized in combination. In this test, the physiologic change of thetest cells caused by the drugs is measured and compared to a baselinemeasurement. A Combination Test can include two or more targeted pathwaydrugs, two or more anti-proliferation drugs, or one or more of each typeof drug.

To demonstrate the embodiments of these tests, 65 experiments on cellsfrom 11 different patients with three different types of cancer wereperformed. Sixteen different drugs affecting 11 different cell pathwayswere tested and two different CReMS types were utilized. A list of thetests whose results are reported in the examples of this application isprovided in Table 1 below:

TABLE 1 List of Tests Performed Example Drug Target Pathway PatientCells Ex. 1 Lapatinib Her2 receptor MAPK, RHO, AKT, B1, B4 FAK1,RAS/RAF, PIK3/PTEN, cellular adhesion Ex. 1 Trastuzumab Her2 receptorMAPK, RHO, AKT, B1, B4 FAK1, RAS/RAF, PIK3/PTEN, Cellular adhesion Ex. 2Paclitaxel TUBB1, BCL2 Apoptotic pathways, B1, B2 cellular adhesion Ex.3 Cetuximab and EGFR MAPK, RHO, AKT, C1, C3 Irionotecan Topoisomerase IFAK1, RAS/RAF, PIK3/PTEN, Apoptotic pathways, cellular adhesion Ex. 4Capecitabine Thymidylate synthase Apoptotic pathways, B2 cellularadhesion Ex. 4 Cetuximab EGFR MAPK, RHO, AKT, B3, B5, C1, FAK1, RAS/RAF,C2, C1, C2 PIK3/PTEN, cellular adhesion Ex. 4 Cisplatin DNA Apoptoticpathways, L1, L2 cellular adhesion Ex. 4 Docetaxel TUBB1, BCL2 Apoptoticpathways, B1, B2, B3, cellular adhesion B4 Ex. 4 Erlotinib EGFR MAPK,RHO, AKT, L1, L2 FAK1, RAS/RAF, PIK3/PTEN, cellular adhesions Ex. 4Fluourouracil Thymidylate synthase Apoptotic pathways, B1, B3 cellularadhesion Ex. 4 Gefitinib EGFR-TK MAPK, RHO, AKT, B1, B2, B3 FAK1,RAS/RAF, PIK3/PTEN, cellular adhesion Ex. 4 GSK1059615 PI3K PI3K/PTEN,cellular B1, B2, B3, adhesion B4, B5, B7 Ex. 4 GSK1120212 MEK1 and MEK 2MEK, cellular adhesion B1, B2, B3, B5, B7, B8 Ex. 4 IrinotecanTopoisomerase I Apoptotic pathways, C1, C2 cellular adhesion Ex. 4Lapatinib Her2 receptor MAPK, RHO, AKT, B2, B3, B5, FAK1, RAS/RAF, B6,B7 PIK3/PTEN, cellular adhesion Ex. 4 Oxiliplatin GG, AG, GNG Apoptoticpathways, C1, C2 cellular adhesion Ex. 4 Paclitaxel TUBB1, BCL3Apoptotic pathways, B3, B4 cellular adhesion Ex. 4 Paclitaxel and TUBB1,BCL2, DNA Apoptotic pathways, L1, L2 Cisplatin cellular adhesion Ex. 4Pazopanib VEGF receptor PI3K/PTEN, RAS/RAF, B1, B2, B3, MAK, MKK,cellular B5, B7, B8 adhesion Ex. 4 Trastuzumab and Her2 receptor MAPK,RHO, AKT, B1, B2, B3, Lapatinib FAK1, RAS/RAF, B4 PIK3/PTEN, cellularadhesion Ex. 4 Topotecan Topoisomerase I Apoptotic pathways, B3 cellularadhesion Ex. 4 Trastuzumab Her2 receptor MAPK, RHO, AKT, B2, B3 FAK1,RAS/RAF, PIK3/PTEN, cellular adhesion Ex. 5 Cetuximab EGFR MAPK, RHO,AKT, B1, B2, B3, (optical, impedance) FAK1, RAS/RAF, B4 PIK3/PTEN,cellular adhesionRationale for Experimental DesignTissue:

Tissues from three of the cancers with the highest occurrence rates werechosen.

Breast Cancer.

Breast cancer cells were utilized for 64% of tests since the breastcancer model is representative of many other cancers in terms ofprogression, varieties of cellular morphologies, variable metabolicrates, and survival and has aberrant molecules and pathways common tocancers found in many other tissues.

Colon and Lung Cancer.

Colon and lung cancer cells were utilized to demonstrate applicabilityof the systems and methods of the disclosure in other significant cancertypes.

Cells:

Cells from eight patients with common clinical presentations ofepithelial cell types for breast cancer were selected for testing. Cellsfrom the patients were obtained using cell sample collection techniquesused regularly by those practiced in the art of tissue collection.

Patient B1:

Cells are derived of a TNM stage IIA, grade 3 primary invasive ductalcarcinoma of the breast in a 61-year-old woman. The cells have adoubling time of approximately 31 hours, appear as enlarged withoccasional amorphous-shaped epithelial cell morphology, and have a veryhigh expression level of ERB B1 and ERB B2 receptors. The EstrogenReceptor (ER), Progesterone Receptor (PR) and Oncogene TP53 status areall three negative.

Patient B2:

Cells are derived of pleural effusion of adenocarcinoma of the breast ofa 51-year old Caucasian woman. The cells have a doubling time ofapproximately 28 hours, appear with invasive, eel-like morphology andhave high expression levels of ERB B1 and slightly elevated above normalERB B2 receptor level, are Estrogen Receptor (ER) negative, ProgesteroneReceptor (PR) negative and have a high Oncogene TP53 status.

Patient B3:

Cells are derived of pleural effusion of adenocarcinoma of the breast ina 43-year-old white woman; approximately 20 hours doubling time,cobblestone epithelial morphology, very high expression levels of ERB B1and ERB B2 receptors, and Estrogen Receptor (ER) negative, ProgesteroneReceptor (PR) negative, and Oncogene TP53 positive status.

Patient B4:

Cells are derived of ascites fluid of invasive ductal carcinoma of thebreast in a 47-year-old black woman; has a doubling time of 110 hours, around, grape-like cluster morphology, has very high expression levels ofERB B1 and ERB B2 receptors, and Estrogen Receptor (ER) positive,Progesterone Receptor (PR) negative, and Oncogene TP53 wild type-lowstatus.

Patient B5:

Cells are derived of primary breast invasive ductal carcinoma in a60-year-old white woman; 28 hours doubling time, mixture of amorphousspreading and invasive morphology, very high expression levels of ERB B1and ERB B2 receptors, and Estrogen Receptor (ER) positive, ProgesteroneReceptor (PR) positive, and Oncogene TP53 positive status.

Patient B6:

Cells are derived of primary breast metaplastic carcinoma TNM stage IVgrade 3 in a 70-year-old black woman; approximately 30 hours doublingtime, roughened spreading morphology, very high expression levels of ERBB1 and ERB B2 receptors, and Estrogen Receptor (ER) negative,Progesterone Receptor (PR) negative, and Oncogene TP53 mutated lowstatus.

Patient B7:

Cells are derived of pleural effusion of invasive ductal carcinoma ofthe breast in a 69-year-old white woman; 30 hours doubling time, smallmosaic epithelial morphology, low expression levels of ERB B1 and ERB B2receptors, and Estrogen Receptor (ER) positive, Progesterone Receptor(PR) positive, and Oncogene TP53 wild type status.

Patient B8:

Cells are derived of pleural effusion of adenocarcinoma of the breast ina 48-year-old white woman; 24 hours doubling time, very small grape-likecluster morphology, low expression level of ERB B1 receptors, highexpression level of ERB B2 receptors, and Estrogen Receptor (ER)negative, Progesterone Receptor (PR) negative, and Oncogene TP53wild-type low status.

Cells from two patients with common clinical presentations of epithelialcell types for colon cancer were selected for testing:

Patient C1:

Cells are derived of a male colorectal carcinoma. The cells have aspheroid volume doubling time of 14 hours, high levels of ERB B1, mutantK-Ras, mutant PIK3CA and oncogeneTP53 positive status.

Patient C2:

Cells are derived of a primary colon adenocarcinoma, grade 2, in a 44year-old Caucasian female. The cells have a spheroid volume doublingtime of 46 hours, high levels of ERB B1, mutant BRAF, and oncogene TP53negative status.

Cells from two patients with common clinical presentations of epithelialcell types for non-small cell lung cancer were selected for testing:

Patient L1:

Cells are derived of pleural effusion of non-small cell lung carcinomaof a 25-year-old male; 48 hours doubling time, epithelial morphology,elevated expression levels of ERB B1 and ERB B2 receptors, PIK3CApositive, and KRAS, BRAF both negative status.

Patient L2:

Cells are derived of a bronchioloalveolar adenocarcinoma of a52-year-old white male; approximately 30 hours doubling time, epithelialmorphology, normal expression levels of ERB B1 and ERB B2 receptors, andBRAF, HRAS, PIK3CA, and KRAS all negative status.

Cell Pathway Targets:

The drugs chosen for these experiments affect eleven cellular pathwayswhich are representative of most cellular regulatory pathways in howthey are extensively interconnected, regulated through binding, involveenzymatic activities such as phosphorylation and de-phosphorylation, andcontrol critical cellular functions.

MAPK. (EGFR, EGFR-TK, HER1, HER 2).

Mitogen-activated protein (MAP) kinases are found in all cell types andare essential serine/threonine-specific protein kinases that respond toextracellular stimuli (mitogens, osmotic stress, heat shock andpro-inflammatory cytokines) and regulate various cellular activities,such as gene expression, mitosis, differentiation, proliferation, andcell survival/apoptosis. Their tight regulation is important tomaintaining cellular viability. The epidermal growth factor receptor(EGFR; ErbB-1; HER1 in humans) is the cell-surface receptor for membersof the epidermal growth factor family (EGF-family) of extracellularprotein ligands. Mutations that lead to EGFR overexpression (known asup-regulation) or over-activity have been associated with a number ofcancers, including lung cancer, anal cancers and glioblastomamultiforme. Mutations, amplifications or mis-regulations of EGFR orfamily members are implicated in about 30% of all epithelial cancers,and it is the target of an expanding class of anticancer therapies.

PI3K/PTEN (Her2, 3, 4, VEGF).

The phosphatidylinositol 3-kinase (PI3K) pathway found in nearly allcell types is critical for cell survival and cell growth, and can beactivated by growth factors binding to cell surface receptors. It is anintricate signaling cascade that is among the most frequently activatedpathways in cancer. It is targeted by genomic aberrations includingmutation, amplification and rearrangement more frequently than any otherpathway in human cancer. VEGF Receptor is expressed across a wide rangeof human tumors and cell lines. Expression of VEGF has been shown tolead to the development and maintenance of a vascular network thatpromotes tumor growth and metastasis. VEGF is expressed in a majority ofnon-small cell lung cancer (NSCLC), colorectal, and other tumors. VEGFis expressed at higher levels as lung cancer progresses. Moreover, alarge and growing body of evidence indicates that VEGF gene expressionis associated closely with poor prognosis.

Cell Adhesion.

Cell adhesion pathways intersect nearly all major physiologicalfunctions. The pathways involve the binding of a cell to a surface,extracellular matrix or another cell using cell adhesion molecules suchas selectins, integrins, and cadherins. Correct cellular adhesion isessential in maintaining multicellular structure. Cellular adhesion canlink the cytoplasm of cells and can be involved in signal transduction.All adhesion is mediated by the cell surface, either directly involvingintegral components of the plasma membrane, or indirectly throughmaterial excreted and deposited on the outside of the cell.

MEK.

MEK is a key protein kinase in the RAS/RAF/MEK/ERK pathway, whichsignals for cancer cell proliferation and survival. MEK is frequentlyactivated in cancer, in particular in tumors that have mutations in theRAS and RAF oncogenes. MEK also regulates the biosynthesis of theinflammatory cytokines TNF, IL-6 and IL-1, which can act as growth andsurvival factors in cancer. The MEK pathway acts as a central axis inthe proliferation of different tumors including melanoma, non-small celllung, head/neck and pancreatic cancers. And MEK inhibition, either aloneor in combination with other agents, is an important therapeuticstrategy in treating cancer.

RHO.

Rho proteins are involved in a wide variety of cellular functions suchas cell polarity, vesicular trafficking, the cell cycle andtranscriptomal dynamics. Rho activation can have a number of differenteffects in cancerous cells. In the initiation of the tumor, modificationof Rho activity can suppress apoptosis and therefore contribute toartificial cell longevity. After natural apoptosis is suppressed,abnormal tumor growth can be observed through the loss of polarity inwhich Rho proteins play an integral role. Next, the growing mass caninvade across its normal boundaries through the alteration of adhesionproteins potentially caused by Rho proteins.

AKT.

AKT is serine/threonine kinase and functions intracellularly as acardinal nodal point for a constellation of converging upstreamsignaling pathways, which involve stimulation of receptor tyrosinekinases such as IGF-1R, HER2/Neu, VEGF-R, PDGF-R, and an assembly ofmembrane-localized complexes of receptor-PI-3K and activation of Aktthrough the second messenger PIP. Because AKT and its upstreamregulators are deregulated in a wide range of solid tumors andhematologic malignancies, and in view of the aforementioned biologicsequelae of this pathway, the AKT pathway is considered a keydeterminant of biologic aggressiveness of these tumors, and a majorpotential target for novel anti-cancer therapies.

FAK1.

The biological importance of Focal adhesion kinase 1 (FAK1)-mediatedsignal transduction is underscored by the fact that this tyrosine kinaseplays a fundamental role in embryonic development, in control of cellmigration, cell cycle progression, and in apoptosis. It plays a centralrole in the survival of anchorage-dependent cells and is essential forintegrin-linked cell migration—the processes that play important rolesin the development of malignancies. FAK is upregulated in a wide varietyof human epithelial cancers, with expression being closely correlated toinvasive potential. Recently, FAK expression has been implicated ineither the progression of tumor cells to malignancy or the pathogenesisof cancer. FAK1 plays a major role in regulating Breast canceranti-estrogen resistance.

RAS/RAF.

The RAS pathway is one of the most frequently deregulated pathways incancer. RAS signals through multiple effector pathways, including theRAF/mitogen-activated protein kinase (MAPK)/extracellularsignal-regulated kinase (ERK) kinase (MEK)/ERK MAPK andphosphatidylinositol 3-kinase (PI3K)-AKT signaling cascades. Theoncogenic potential of these effector pathways is illustrated by thefrequent occurrence of activating mutations in BRAF and PIK3CA as wellas loss-of-function mutations in the tumor suppressor PTEN, a negativeregulator of PI3K. Owing to this important role of Ras in tumorigenesis,the Ras-signalling pathway has attracted considerable attention as atarget for anticancer therapy.

MAK Pathway.

Metastasis-associated kinase (MAK) is a novel regulator of thetranscription factors required for cell growth. Inhibition of thispathway leads to cell cycle arrest activity.

MKK.

Mitogen-activated protein kinase kinases (MKK) signaling pathways havebeen to both the transcriptional and the post-translational regulationof vital cellular processes including cell differentiation,proliferation, motility and survival. Since MKK signaling pathways playessential roles in modulating the release of, and the response to VEGF,it is believed that MKK plays an important role in promoting tumorvascularization.

Apoptotic Pathways.

Activation of apoptosis pathways is a key mechanism by which cytotoxicdrugs kill tumor cells. Apoptosis occurs through two main pathways. Thefirst, referred to as the extrinsic or cytoplasmic pathway, is triggeredthrough the Fas death receptor, a member of the tumor necrosis factor(TNF) receptor superfamily. The second pathway is the intrinsic ormitochondrial pathway that when stimulated leads to the release ofcytochrome-c from the mitochondria and activation of the death signal.Both pathways converge to a final common pathway involving theactivation of a cascade of proteases called caspases that cleaveregulatory and structural molecules, culminating in the death of thecell. Defects in apoptosis signaling contribute to resistance of tumors.

Therapeutic Agent:

The therapeutic agents chosen include ones representative of smallmolecule drugs and those derived from antibodies. The therapeutic agentstested include some with mechanisms of action designed to shut down aspecific pathway functional within a cell and others designed to causecell apoptosis.

Cetuximab.

Cetuximab (Erbitux) is a chimeric (mouse/human) monoclonal antibody, anepidermal growth factor receptor (EGFR) inhibitor, given by intravenousinfusion for treatment of metastatic colorectal cancer and head and neckcancer. When growth factors bind to their receptors on the surface ofthe cell, the receptors give a signal that causes cells to divide. Somecancers are caused by mutated receptors that give a signal to divideeven without growth factor. That causes the cells to divideuncontrollably. Cetuximab binds to receptors like that and turns offthat signal.

Erlotinib.

Erlotinib hydrochloride (Tarceva) is a drug used to treat non-small celllung cancer, pancreatic cancer and several other types of cancer. It isa reversible tyrosine kinase inhibitor, which acts on the epidermalgrowth factor receptor (EGFR). Erlotinib specifically targets theepidermal growth factor receptor (EGFR) tyrosine kinase, which is highlyexpressed and occasionally mutated in various forms of cancer. It bindsin a reversible fashion to the adenosine triphosphate (ATP) binding siteof the receptor.

Lapatinib.

Lapatinib (Tykerb/Tyverb) is an orally active drug for breast cancer andother solid tumours. It is a dual tyrosine kinase inhibitor whichinterrupts the HER2 growth receptor pathway. It is used in combinationtherapy for HER2-positive breast cancer. Lapatinib inhibits the tyrosinekinase activity associated with two oncogenes, EGFR (epidermal growthfactor receptor) and HER2/neu (Human EGFR type 2). Over expression ofHER2/neu can be responsible for certain types of high-risk breastcancers in women.

Trastuzumab.

Trastuzumab (Herceptin) is a monoclonal antibody that interferes withthe HER2/neu receptor. Its main use is to treat certain breast cancers.When it binds to defective HER2 proteins, the HER2 protein no longercauses cells in the breast to reproduce uncontrollably.

Docetaxel.

Docetaxel (Taxotere) is a clinically well-established anti-mitoticchemotherapy medication (that is, it interferes with cell division). Itis used mainly for the treatment of breast, ovarian, prostate, andnon-small cell lung cancer. Docetaxel is of the chemotherapy drug class;taxane, and is a semi-synthetic analogue of paclitaxel (Taxol).

GSK1059615.

A phosphoinositide 3-kinase inhibitor (PI3K inhibitor) is a potentialmedical drug that functions by inhibiting a phosphoinositide 3-kinaseenzyme which is part of the PI3K/AKT/mTOR pathway, which plays a keyrole in cancer. Inhibiting this pathway often suppresses tumor growth.

GSK1120212.

GSK1120212 is a potent and selective allosteric inhibitor of the MEK1and MEK2 (MEK1/2) enzymes with promising antitumor activity.

Pazopanib.

Pazopanib (Votrient) is a potent and selective multi-targeted receptortyrosine kinase inhibitor of VEGFR-1, VEGFR-2, VEGFR-3, PDGFR-α/β, andc-kit that blocks tumor growth and inhibits angiogenesis.

Paclitaxel.

Paclitaxel is a mitotic inhibitor used to treat patients with lung,ovarian, breast, head and neck cancer, and advanced forms of Kaposi'ssarcoma. Paclitaxel stabilizes microtubules and as a result, interfereswith the normal breakdown of microtubules during cell division. Togetherwith docetaxel, it forms the drug category of the taxanes.

Fluorouracil.

Fluorouracil (5-FU or f5U) (Adrucil, Carac, Efudix, Efudex andFluoroplex) is a drug that is a pyrimidine analog which is used in thetreatment of cancer. It is a suicide inhibitor and works throughirreversible inhibition of thymidylate synthase. It belongs to thefamily of drugs called antimetabolites.

Capecitabine.

Capecitabine (Xeloda) is an orally-administered chemotherapeutic agentused in the treatment of metastatic breast and colorectal cancers.Capecitabine is a prodrug, that is enzymatically converted to5-fluorouracil in the tumor, where it inhibits DNA synthesis and slowsgrowth of tumor tissue.

Topotecan.

Topotecan (Hycamtin) is a chemotherapeutic agent that is a topoisomeraseinhibitor. It is used to treat ovarian cancer and lung cancer, as wellas other cancer types. Topoisomerase-I is a nuclear enzyme that preventsDNA replication, and ultimately leads to cell death. This process leadsto breaks in the DNA strand resulting in apoptosis.

Irinotecan.

Irinotecan (Camptosar) is a drug used for the treatment of colon cancer.Irinotecan is activated by hydrolysis to SN-38, an inhibitor oftopoisomerase I. The inhibition of topoisomerase I by the activemetabolite SN-38 eventually leads to inhibition of both DNA replicationand transcription.

Oxaliplatin.

Oxaliplatin is a coordination complex that is used in cancerchemotherapy. These platinum-based drugs are usually classified asalkylating agents. Oxaliplatin is an alkylating agent which functions byforming both inter- and intra-strand cross links in DNA. Cross links inDNA prevent DNA replication and transcription, resulting in cell death.

Cisplatin.

Cisplatin (Platin) is used to treat various types of cancers, includingsarcomas, some carcinomas (e.g. small cell lung cancer, and ovariancancer), lymphomas, and germ cell tumors. It was the first member of aclass of platinum-containing anti-cancer drugs, which now also includescarboplatin and oxaliplatin. These platinum complexes react in vivo,binding to and causing crosslinking of DNA, which ultimately triggersapoptosis.

CReMS Types

Two types of CReMS, an optical biosensor and an impedance biosensor,were utilized to measure the physiologic response of cells during thetests and to demonstrate how the amount of physiologic change thatoccurs can be measured on different types of CReMS.

Prediction Criteria

The amount of physiologic change caused during a CELx test by inhibitionof a targeted pathway or an apoptotic pathway was recorded into one ofthree categories:

-   -   1) Non-responder: <5% reduction of the cell index by the highest        physiologically relevant concentration of the two drugs as        compared to the untreated control cells. This result would        indicate that the patient will not respond to the tested drug        combination;    -   2) Responder (weak): Between 5-50% reduction of the cell index        by the drugs at any level of concentration. This would indicate        that the patient will respond to the combination of test drugs        to some degree.    -   3) Responder (strong): >50% reduction of the cell index by the        drugs at any level of concentration. This would indicate that        the patient will respond to the test drug.

Cell index using an impedance or optical biosensor is calculated using abaseline starting point of impedance measurement or refractive indexmeasurement. The baseline starting point impedance or refractive indexis a physical observable and an indication of the health, viability, andphysiologic status of a cell prior to any treatment with drug or otherperturbant. Addition of drug or perturbant causes the baseline readingof impedance or refractive index to change in temporal patternsreflective of the specificity of the cellular physiologic changeexperienced by the cell.

Example 1 Pathway Shutdown Tests Showing Differentiated Response of TwoPatients to Two Drugs

A CELx Pathway Shutdown test was performed using cells from two HER2overexpressing breast cancer patients (Patient B1 and B4), two drugs(Lapatinib and Trastuzumab) that are indicated for HER2 positive breastcancers, and human epidermal growth factor (EGF). The physiologic changeof the B1 and B4 cells during the test was measured with an impedancebiosensor CReMS and the output from the CReMS is recorded in FIGS. 1Aand 1B. The comparison of the CELx test results and the third partyclinical reference is recorded in FIG. 1C. This example illustrates howthe CELx test is able to predict the responsiveness that a patient willhave to different targeted pathway drugs by using a CReMS to measure thephysiological change in a patient's cells continuously over a period ofseveral hours. This example also illustrates how the presence of agenetic biomarker, in this case an overexpressing HER2 gene, is not asufficient condition to predict efficacy of the drug.

Materials and Methods

CReM and Microplate:

A 4″×6″, 96-well impedance microplate was placed into a Roche AppliedScience (Indianapolis, Ind.) xCELLigence SP impedance biosensor designedto maintain constant voltage while measuring simultaneously theimpedance of every well. The change in impedance for a particular wellis proportional to the number of cells and type of attachment the cellshave with the impedance microplate. Changes in impedance indicate aresponse to perturbation of these small cell populations.

Cells:

Cells from Patient B1 and B4 were utilized. The cells were received at−80° C., thawed and cultured according to standard human epithelial cellhandling procedure, typically in T75 culture flasks containing bufferedmedia with serum at 37° C., 5% CO2. Prior to addition to the impedancemicroplate, the cells were removed from their growth container withversene, counted, and re-suspended in media without serum or othergrowth factors.

Buffers and Reagents:

Standard media, serum, antibiotics (e.g. penicillin, streptomycin), andother buffers were purchased and used as delivered from ATCC (Manassas,Va., USA) or Life Technologies (Grand Island, N.Y.). Additional growthfactor (mature human EGF ca6KDa) was purchased from R&D Systems(Minneapolis, Minn.) and prepared in buffered cell media without growthfactors or serum. The therapeutic agent Lapatinib, a small moleculedrug, was purchased from Selleck Chemicals (TX, USA); trastuzumab, anantibody drug, was obtained from a clinical dispensary.

Procedure:

Between 6,000-12,000 cells in each well were seeded onto the impedancemicroplate containing 120 uL standard media with serum. The solution wasreplaced with media containing no serum to synchronize the cells withrespect to physiologic state and pathway stimulation. Twenty microlitersof drugs were added to the no-serum media two hours in advance ofpathway stimulation. Pathway stimulation was initiated using EC80 dosesof receptor ligand (typically 6 nM in 20 uL). The CReMS recording ofphysiologic change was maintained continuously for several hours frombuffer exchange through complete cellular response to the pathwaystimulation. The pathway test was performed at 37° C., 5% CO2 and at arelative humidity 75%.

The CReMS recorded data on a continuous basis throughout the test, wherethe data represented the effects of the two therapeutic agents on the B1and B4 cells.

Results:

FIGS. 1A and 1B present the data collected during the CELx test on theB1 and B4 cells respectively with the antibody drug trastuzumab and thesmall molecule drug lapatinib. The data collected by the impedance CReMSis represented in each figure with time in minutes on the X-axis and thecell index on the Y-axis. The cell index represents the physiologicchange of the Bland B4 cells during the test.

Results indicate that stimulation of the full pathway with a ligandreceptor and no drug added generated the highest cell index. After thedrug trastuzumab was added to the stimulated B1 cells, the cell index ofthe test cells changed less than 5%, indicating the B1 test cells wereunaffected by the addition of the trastuzumab. Conversely, after thedrug lapatinib was added to the B1 cells, the cell index for the testcells decreased by over 50%, indicating that the activity within thetargeted pathway is diminished significantly. After the drugs, lapatiniband trastuzumab were each added to separate samples of B4 cells, thecell index of each test cell sample decreased by over 50%. Thisindicated that the activity within the targeted pathway of each testcell sample was diminished significantly.

Based on these results, the CELx Pathway Shutdown test shown in FIG. 1Apredicts that Patient B1 will not respond to trastuzumab but willrespond to Lapatinib. The results shown in FIG. 1B also predict thatPatient B4 would respond to both trastuzumab and lapatinib. Thecomparison of the CELx test prediction and the result recorded by thirdparty clinical reference is shown in FIG. 1C; it shows that the CELxtest accurately predicted the results recorded by the clinical referencestandard, where Patient B1 was found unresponsive to trastuzumab andresponsive to lapatinib and Patient B4 was found responsive to both.

Discussion:

In the present example of this invention, the CELx test accuratelypredicted the efficacy of two drugs, trastuzumab and lapatinib, usingcells Patients B1 and B4. The B1 and B4 cells responded to stimulationof the HER2 pathway with a receptor ligand, indicating that the patientcould respond to a drug able to shut down activity within that pathway.In this example, the B1 cells demonstrate a differentiated response tothe two drugs, despite the drugs having similar mechanisms of action.Patient B1 was found to be responsive to lapatinib and non-responsive totrastuzumab.

This example illustrates how the CELx test can be applied to differenttypes of therapeutic agents, including ones that work at the cellsurface, as in the case of trastuzumab, an antibody drug, or ones thatwork in the cytoplasm, as in the case of the kinase inhibitor drug,lapatinib. It also illustrates how the systems and methods of thedisclosure are effective to detect changes in response to drugs thattarget the MAPK, RHO, AKT, FAK1, RAS/RAF, PIK3 and cell adhesionpathways. This example also illustrates the principle that knowledge ofthe presence of a relevant genetic biomarker, in this case anoverexpressing HER2 gene, is not a sufficient condition to predictwhether the drug will function according to its intended mechanism ofaction. In this example, the drug trastuzumab does not always shut downthe HER2 growth factor signaling pathway in every Her2 positive cancercell type, as it is intended to. Despite similar genetic profiles,Patients B1 and B4 respond differently to trastuzumab as confirmed bythe CELx test. Conversely, an embodiment of the method of the inventionaccurately predicts that another drug, Lapatinib, working at the HER2site, is able to shut down the pathway as designed for both patients.The results of this example correlate with the response reported by athird party, confirming the ability to use the measurement ofphysiological change in a patient's diseased cells to predict whether atherapeutic will provide the intended efficacy. With the presentinvention, a physician selects a treatment for a breast cancer patientbased on the actual responsiveness of the tumor cells to the drugs.

Example 2 Anti-Proliferative Tests Showing Differentiated Response ofTwo Patients to One Drug

A CELx Anti-Proliferative test was performed using cells from two breastcancer patients (Patients B1 and B2) and the drug Paclitaxel. Thephysiologic change of the B1 and B2 cells during the test was measuredwith an impedance biosensor CReMS and the output from the CReMS isrecorded in FIGS. 2A and 2B. The comparison of the CELx test results andthe third party clinical reference is recorded in FIG. 2C. This exampledemonstrates the ability of the CELx test to predicting the efficacy ofa therapeutic agent by measuring the physiologic change over the courseof several days in a patient's cancer cells after an anti-proliferativedrug is introduced. This example also demonstrates the role of abaseline, in this case, untreated patient cells, in measuring theresults. In addition, the results recorded for patient B2 demonstratethe importance of monitoring the cells' physiological response on acontinuous basis over several days because of changes that can occurover time in a cell's responsiveness to a drug.

Materials and Methods

CReMS, Microplate, Reagents, and Buffers:

The CReMS, microplate, reagents, and buffers used in Example 1 are thesame as those employed in Example 2, except for the therapeutic agenttested. In Example 2, the therapeutic agent, paclitaxel, was tested.Paclitaxel was purchased from Selleck Chemicals (TX, USA).

Cells:

Breast Cancer cells from Patients B1 and B2 were utilized and handled inthe same manner as described in Example 1.

Procedure:

Between 6,000-12,000 cells in each well were seeded onto the impedancemicroplate containing 120 uL settling media with serum. Fortymicroliters of the drug paclitaxel were added to one set each of the B1and B2 cells; another control set of B1 and B2 cells received no drug.The CReMS recording of physiologic change was maintained continuouslyfrom when the cells were first seeded on the microplate through completecellular response, which was between 48-72 hours. The test was performedat 37° C., 5% CO2 and at 75% relative humidity.

Results:

FIGS. 2A and 2B present the data collected during the CELx test on theB1 and B2 cells with the drug Paclitaxel. The data collected by theimpedance CReMS is represented in the figure with time in hours on theX-axis and the cell index on the Y-axis. The cell index represents thephysiologic change of the B1 and B2 cells during the test. An increasein the cell index is generally an indication of increase in cellproliferation. Whereas a decrease in long term cell index is generallyindicative of loss of cell viability or live cell number decrease. TheB2 test cells showed initial responsiveness to Paclitaxel, as reflectedin the significant decrease in CReM output compared to the B2 controlcells, but after roughly 24 hours, the CReM output reverses, indicatingthat the test cells begin proliferating and are no longer responsive tothe drug. The B1 test cells show immediate and continuous responsivenessto Paclitaxel, as reflected in the decrease in CReM output compared tothe B1 control cells throughout the test period. The CELx test resultspresented in FIGS. 2A and 2B predict that both patients B1 and B2 willrespond to paclitaxel. The comparison of the CELx test prediction andthe result recorded by third party clinical reference is shown in FIG.2C; it shows that the CELx test accurately predicted the resultsrecorded by the clinical reference standard, where Patients B1 and B2were both found responsive to paclitaxel.

Discussion:

In the present example, the CELx test accurately predicted the efficacyof an anti-proliferative drug, paclitaxel, with two breast cancerpatients, B1 and B2. Additionally, the CELx test result for Patient B2indicated that resistance to paclitaxel develops in the short-term,illustrating the importance of monitoring the cells' physiologicalresponse on a continuous basis over an extended period of time. Thisresult is important because one of the major issues with drug therapy isthe rapid development of resistance to a drug. Time is lost when apatient is prescribed an ineffective therapy. Besides increasing therisk of chemotoxicity and incurring the common side effects ofchemotherapy, in many cases, treatment with one drug eliminates thepossibility of treatment with another drug that may have been moreeffective.

Example 3 Combination Tests Showing Response of Two Patients to TwoDrugs Taken Together

A CELx Combination test was performed using cells from two colon cancerpatients (Patients C1 and C2), EGF, and a combination of two drugsindicated for colon cancer, Cetuximab and Irinotecan. The physiologicchange of the C1 and C2 cells during the test was measured with animpedance biosensor CReMS and the output from the CReMS is recorded inFIGS. 3A and 3B. The comparison of the CELx test result and the thirdparty clinical reference is recorded in FIG. 3C. This exampledemonstrates how the CELx test is able to predict the responsivenessthat individual patients will have to a combination of two or more drugsin a way that cannot be done using genetic testing or expressionprofiling. The test also illustrates how the CELx test operates withcolon cancer cells, in addition to breast cancer cells.

Materials and Methods

CReMS, Microplate, Reagents, and Buffers:

The CReMS, microplate, reagents, and buffers used in Examples 1 and 2are the same as those employed in Example 3, except for the therapeuticagent used. In Example 3, two therapeutic agents, cetuximab andirinotecan, were tested. Irinotecan was purchased from Selleck Chemicals(TX, USA) and cetuximab was obtained from a clinical dispensary.

Cells:

Colon cancer cells from Patients C1 and C2 were utilized and handled inthe same manner as described in Example 1.

Procedure:

Between 6,000-12,000 cells in each well were seeded into the impedancemicroplate containing 120 uL settling media with serum. The solution wasreplaced with media containing no serum to synchronize the cells withrespect to physiologic state. Twenty microliters each of irinotecan andcetuximab was added to one set each of the C1 and C2 cells; anothercontrol set of C1 and C2 cells received no drugs. The CReMS recording ofphysiologic change was maintained continuously from when the cells werefirst seeded on the microplate through complete cellular response, whichwas between 48-72 hours. The test was performed at 37° C., 5% CO2 and at75% relative humidity.

Results:

FIGS. 3A and 3B present the data collected during the CELx test on theC1 and C2 cells and the combination of the antibody drug cetuximab andthe small molecule drug irinotecan. The data collected by the impedanceCReMS is represented in the figures with time in hours on the X-axis andthe cell index on the Y-axis. The cell index represents the physiologicchange of the C1 and C2 cells during the test. Results show that theuntreated control C1 and C2 cells generated the highest cell index.Results after the two drugs are added to the C1 and C2 test cells show areduction of the cell index for each cell sample of greater than 50%.These results predict that both patients C1 and C2 will respond to thecombination of cetuximab and irinotecan. The comparison of the CELx testprediction and the result recorded by third party clinical reference isshown in FIG. 3C; it shows that the CELx test accurately predicted theresults recorded by the clinical reference standard, where Patients C1and C2 were both found responsive to the cetuximab and irinotecancombination.

Discussion:

In the present example, the CELx test accurately predicted the efficacyof two drugs, cetuximab and irinotecan, with two colon cancer patients,C1 and C2. However, even though the overall results for Patient C1 withthe two drugs showed a greater than 50% reduction in the cell index, theCELx test result indicated that one of the drugs, cetuximab, did notcause a physiologic change in Patient C1's cells. This would suggestthat the entire therapeutic benefit of the drug combination in PatientC1 was likely due to the irinotecan. If a physician knew that only onedrug within a combination therapy was effective, in this caseirinotecan, they would then only prescribe the efficacious drug. TheCELx test result indicated that Patient 2 was responsive to eachindividual drug, suggesting the combination of drugs would be moreefficacious than a use of only a single drug.

The results illustrate how the CELx test is able to predict theresponsiveness of individual patients to a combination of two or moretherapeutic agents. The test illustrates how the CELx test operates withcolon cancer cells. It further illustrates the physiologicalresponsiveness of cancer cells to different types of drugs, in thiscase, the antibody drug cetuximab, that works by binding to the cellsurface, and an apoptotic pathway inhibitor, in this case irinotecan,which works by binding to the cell nucleus. And it also illustrates thephysiological responsiveness of cancer cells to drugs that target theMAPK, RHO, AKT, FAK1, RAS/RAF, PIK3, and cell adhesion pathways and anapoptotic pathway. The result would allow a physician to select a moreefficacious treatment for a colon cancer patient

Example 4 Additional CELx Tests Using Different Drugs

Fifty-one CELx Pathway Shutdown and Anti-Proliferative single drug testswere performed using some of the cell and drug combinations possiblefrom a selection of 11 different patient cells (breast cancer cells fromPatients B1, B2, B3, B4, B5, B6, B7), colon cancer cells from PatientsC1 and C2, and lung cancer cells from Patients L1 and L2) and 15different drugs (capecitabine, cetuximab, docetaxel, fluorouracil,gefitinib, GSK1059615, GSK1120212, lapatinib, paclitaxel, pazopanib,trastuzumab, topotecan, cisplatin, erlotinib, and oxiliplatin). Six CELxCombination tests were performed, two with the drug combination ofpaclitaxel and cisplatin and Patient L1 and L2 cells, and four with thedrug combination of trastuzumab and lapatinib and Patient B1, B2, B3,and B4 cells. The physiologic change of the cells and drugs tested wasmeasured with an impedance biosensor CReMS and the summary output fromthe CReMS is recorded in FIG. 4. The correlation between these CELx testresults and the third party clinical reference is recorded in FIG. 7.

Materials and Methods

CReMS, Microplate, Reagents, and Buffers:

Each of the 57 tests listed in FIG. 4 relied upon the same CReMS,microplate, reagents, and buffers as those described in the Examples1-3.

Cells:

Cells from Patients B1, B2, B3, B4, B5, B6, B7, C1, C2, L1, and L2 wereutilized and handled in the same manner as described in Example 1.

Procedures:

In those experiments involving targeted pathway drugs (cetuximab,gefitinib, GSK1059615, GSK1120212, lapatinib, pazopanib, trastuzumab,and erlotinib) the procedures described in Example 1 were utilized. Inthose experiments involving anti-proliferative drugs (capecitabine,docetaxel, fluorouracil, paclitaxel, topotecan, cisplatin, andoxiliplatin), the procedures described in Example 2 were utilized. Inthose experiments involving a combination of drugs, the proceduresdescribed in Example 3 were utilized. The list of patient cells and thedrug tested with the cells is characterized in FIG. 4.

Results:

The summary results of the 57 CELx tests performed on the variouscombinations of cells and drugs listed is shown in FIG. 4. For eachexperiment, the change of the test cells' physiologic response comparedto its control cells was calculated. Each box in FIG. 4 classifies thechange in physiologic response measured in each experiment as eitherbeing greater than 50%, between 5%-50%, or less than 5%. The series oftests represented in FIG. 4 illustrate the CELx test's ability tomeasure the physiologic change that occurs in a variety of common cancercell types after they are exposed to wide range of drugs that target awide range of cellular pathways. The comparison of the CELx testprediction and the result recorded by third party clinical reference isshown in FIG. 7; it shows the CELx test result correlated with the thirdparty clinical reference reported for the patient and drug combination.

Discussion:

In the 57 tests described in this example, the invention describedherein demonstrated efficacy with:

Colon, breast, and lung cancer cells;

Targeted pathway drugs that inhibit the MAPK, RHO, AKT, FAK1, RAS/RAF,PI3K, MAK, MKK, MEK and cell adhesion pathways through targets thatinclude EGFR, EGFR-TK, PI3K, MEK1, MEK2, HER2 receptor, and VEGFR; and

Anti-proliferative drugs that target apoptotic pathways through targetsthat include Topoisomerase I, TUBB1, BCL2, DNA, purine crosslinking (GG,AG, GNG), and thymidylate synthase.

Each of the CELx test results except one correlated with the results forthis Patient cell and drug combination.

Example 5 Concordance Tests Between the Results Produced from DifferentCReMS

A CELx Pathway Shutdown test was performed using cells from four breastcancer patients (Patient B1, B2, B3, B4) with overexpressing epidermalgrowth factor (EGF) receptors, one drug cetuximab, and human epidermalgrowth factor (EGF). The physiologic change of the four patients' cellsduring the test was measured with an impedance biosensor CReMS and anoptical biosensor CReMs to demonstrate the correlation of the resultsproduced from the two different CReMS. The output from the CReMS isrecorded in FIG. 5. This example illustrates how the CELx test is ableto use two different CReMS to obtain the same measurement ofphysiological change in a patient's cells.

Materials and Methods

CReMS and Microplate:

Two different CReMS were used in this example. In one series of tests, a4″×6″, 96-well impedance microplate was placed into a Roche AppliedScience (Indianapolis, Ind.) xCELLigence SP impedance biosensor designedto maintain constant voltage while measuring simultaneously theimpedance of every well. The change in impedance for a particular wellis proportional to the number of cells and type of attachment the cellshave with the impedance microplate. Changes in impedance indicate aresponse to perturbation of these small cell populations. In the otherseries of tests, a 4″×6″, 384-well optical microplate was placed into aPerkinElmer Instruments (Waltham, Mass.) EnSpire Multimode opticalbiosensor designed to scan 850 nanometer near infrared reflected lightin each well. The change in reflected wavelength for a particular wellis proportional to the number of cells and type of attachment the cellshave with the optical microplate. Changes in reflected wavelengthindicate a response to the perturbation of the small cell populations inthe well.

Reagents and Buffers:

The reagents and buffers used in Example 1 are the same as thoseemployed in Example 5, except for the therapeutic agent employed. InExample 5, the therapeutic agent cetuximab was tested. Cetuximab wasacquired from a medical dispensary.

Cells:

Breast cancer cells from Patients B1, B2, B3 and B4 were utilized inboth set of tests and handled in the same manner as described in Example1.

Procedure:

In the set of tests performed with the impedance biosensor CReMS,between 6,000-12,000 cells in each well were seeded onto the impedancemicroplates containing 120 uL settling media with serum. Fortymicroliters of the drug cetuximab was added to the no-serum mediacontaining one set each of the B1, B2, B3, and B4 patient cells twohours in advance of pathway stimulation; another control set of B1, B2,B3 and B4 cells received no drug. Pathway stimulation was initiatedusing EC80 doses of receptor ligand (6 nM in 20 uL). The impedance CReMSrecording of physiologic change was maintained continuously from whenthe cells were first seeded on the microplates through complete cellularresponse, which ranged between 20-48 hours. The test was performed at37° C., 5% CO2 and at 75% relative humidity.

In the set of tests performed with the optical biosensor CReMS, between6,000-12,000 cells in each well were seeded onto the optical microplatescontaining 60 uL settling media with serum. Twenty microliters of thedrug cetuximab was added to the no-serum media containing one set eachof the B1, B2, B3, and B4 patient cells two hours in advance of pathwaystimulation; another control set of B1, B2, B3 and B4 cells received nodrug. Pathway stimulation was initiated using EC80 doses of receptorligand (6 nM in 20 uL). The optical CReMS recording of physiologicchange was maintained continuously from when the cells were first seededon the microplates through complete cellular response, which rangedbetween 20-48 hours. The tests was performed at 25° C.-30° C., <5% CO2and at 30% relative humidity.

Results:

FIG. 5 shows the summary results of the eight CELx tests performedseparately on cells from four breast cancer patients (B1, B2, B3, andB4) with the drug cetuximab and EGF. One set of tests on cells B1, B2,B3, and B4 was performed using an optical biosensor CReMS and anotherset of tests on the same cells was performed using an impedancebiosensor CReMS. The results are presented in a summary fashion showingthe range of percentage change in output recorded by the CReMS. For eachpatient cell tested, the amount of physiologic change recorded by eachCReMS was identical. These results illustrate that the CELx test methodcan utilize different types of CReMSs that measure different physiologicchanges in cells.

Discussion:

In the present example, a CELx Test was performed on two different CReMSthat have different transducer interfaces to measure cellularphysiologic change. Despite the significant differences in the devicesemployed for acquiring the physiological response to treatment, theoptical biosensor CReMS and the impedance biosensor CReMS providedidentical results for each of the patient samples. This result isimportant for the extension of the present invention to many CReMS typesand illustration of the universality of the present invention of usingan individual patient's cellular physiologic change to predicttherapeutic response to drugs.

Summary of Examples Summary of CELx Test Results and ClinicalPredictions

The summary results of all 65 total CELx tests described in Examples 1-4is presented in FIG. 6. The correlation (either 0% or 100%) between theCELx test results described in FIG. 6 and results from third partyclinical references that recorded the patient's responsiveness to asingle drug or drug combination is shown in FIG. 7. In all 65 testsexcept one, the CELx test prediction and the third party measurementgenerated the same result, illustrating the power of the CELx test topredict breast, lung, and colon patient response to 16 different drugsthat target a wide range of cellular pathways.

The CELx test predictions for the various patient cancer cells tested inExamples 1-4 versus the third party record is provided in FIGS. 8A, 8B,8C and 8D. A CELx test result that accurately predicts that a patientwould respond to a drug or drug combination is denoted as a TruePositive (TP) result. An accurate prediction that a patient would notrespond to a drug or drug combination is denoted as a True Negative (TN)result. An inaccurate prediction that a patient would respond to a drugor drug combination is denoted as a False positive (FP) and aninaccurate prediction that a patient would not respond to a drug isdenoted as a False Negative (FN).

FIG. 8A records the comparison of results for all tests performed inExamples 1-4 with the 12 cancer patient cells that were tested singly orin combination with 16 different drugs versus the third party record.FIG. 8B records the comparison of results for the eight breast cancerpatient cells that were tested singly and in combination with thirteendifferent drugs versus the third party record. FIG. 8C records thecomparison of results for the two different colon cancer patient cellsthat were tested singly and in combination with three different drugs.FIG. 8D records the comparison of results for the two different lungcancer patient cells that were tested singly and in combination withthree different drugs. In each Figure, the CELx tests are shown topredict accurately whether a patient will or will not respond to aparticular drug or combination of drugs except in one case In FIG. 8B,it can be seen that one patient breast cancer cell sample that wasexpected to be a responder to gelfitinib did not show a response in theCReMS testing.

The sensitivity and specificity of the CELx test for the patient cellsand drug tested in Examples 1-4 as well as for the sub-groups ofpatients, drugs, pathways, and CReMS types tested is provided in FIG. 9.Overall and within each of the sub-groups studied, the CELx testgenerated high sensitivity (98%+) and specificity (99.9%+). Theseresults illustrate the predictive power of the test across the differentcancer cell types, drug types, CReMS types, and pathways targeted in thetests described in Examples 1-4.

What is claimed:
 1. A method of treating a human subject diagnosed withcancer, the method comprising: administering to the subject a firstagent that is a Human Epidermal growth factor Receptor (HER) familytargeted therapeutic that has been determined to be therapeuticallyactive in the signaling pathway it is intended to address in thesubject's cancer cells, by a method comprising: culturing a samplecomprising viable cancer cells obtained from the subject; contacting thesample with the first agent and with a second agent that is known toselectively affect the same signaling pathway the first agent isintended to address, so as to upregulate or downregulate the signalingpathway as measured by an effect on cell adhesion or attachment, toproduce a sample contacted with both the first agent and the secondagent; continuously measuring cell adhesion or attachment of viableprimary or metastatic cancer cells in the sample contacted with both thefirst agent and the second agent, relative to a sample of viable primaryor metastatic cancer cells obtained from the subject which sample iscontacted with the first agent or the second agent alone; determining bymathematical analysis of the continuous measurements an output value,expressed as a percentage, that characterizes whether a change in celladhesion or attachment has occurred in the sample contacted with boththe first agent and the second agent, as compared to the samplecontacted with the first agent or the second agent alone; andadministering the first agent to the subject wherein the output valuethat characterizes the change in cell adhesion or attachment is equal toor greater than 50%, indicating the first agent is therapeuticallyactive in the cell signaling pathway of the subject's cancer cells. 2.The method of claim 1, wherein the HER family targeted therapeutic isselected from a list consisting of neratinib, gefitinib, erlotinib,cetuximab, panitumumab, trastuzumab, lapatinib, and pertuzumab.
 3. Themethod of claim 2, wherein the HER family targeted therapeutic istrastuzumab.
 4. The method of claim 2, wherein the HER family targetedtherapeutic is lapatinib.
 5. The method of claim 2, wherein the HERfamily targeted therapeutic is pertuzumab.
 6. The method of claim 2,wherein the HER family targeted therapeutic is cetuximab.
 7. The methodof claim 1, wherein the second agent is neuregulin.
 8. The method ofclaim 1, wherein the second agent is heregulin.
 9. The method of claim1, wherein the second agent is an epidermal growth factor.
 10. Themethod of claim 1, wherein cell adhesion or attachment is measured usingan impedance biosensor or an optical biosensor.
 11. The method of claim1, wherein the change in cell adhesion or attachment is assessed usingEuclidean analysis.
 12. The method of claim 1, wherein the cancer isbreast cancer.
 13. The method of claim 1, wherein the sample is culturedin a media free of serum.
 14. The method of claim 13, wherein the mediafree of serum further comprises at least one growth factor.
 15. Themethod of claim 13, wherein the media free of serum further comprises atleast one anti-apoptotic agent.
 16. The method of claim 1, wherein thesample consists essentially of viable primary or metastatic cancer cellsobtained from the subject and wherein the sample is cultured in a mediafree of serum.
 17. The method of claim 16, wherein the media free ofserum further comprises at least one growth factor.
 18. The method ofclaim 16, wherein the media free of serum further comprises at least oneanti-apoptotic agent.